unofficial mirror of guix-patches@gnu.org 
 help / color / mirror / code / Atom feed
blob f84306b6b9119e29bebc606d13c0405e95412185 966369 bytes (raw)
name: gnu/packages/bioinformatics.scm 	 # note: path name is non-authoritative(*)
    1
    2
    3
    4
    5
    6
    7
    8
    9
   10
   11
   12
   13
   14
   15
   16
   17
   18
   19
   20
   21
   22
   23
   24
   25
   26
   27
   28
   29
   30
   31
   32
   33
   34
   35
   36
   37
   38
   39
   40
   41
   42
   43
   44
   45
   46
   47
   48
   49
   50
   51
   52
   53
   54
   55
   56
   57
   58
   59
   60
   61
   62
   63
   64
   65
   66
   67
   68
   69
   70
   71
   72
   73
   74
   75
   76
   77
   78
   79
   80
   81
   82
   83
   84
   85
   86
   87
   88
   89
   90
   91
   92
   93
   94
   95
   96
   97
   98
   99
  100
  101
  102
  103
  104
  105
  106
  107
  108
  109
  110
  111
  112
  113
  114
  115
  116
  117
  118
  119
  120
  121
  122
  123
  124
  125
  126
  127
  128
  129
  130
  131
  132
  133
  134
  135
  136
  137
  138
  139
  140
  141
  142
  143
  144
  145
  146
  147
  148
  149
  150
  151
  152
  153
  154
  155
  156
  157
  158
  159
  160
  161
  162
  163
  164
  165
  166
  167
  168
  169
  170
  171
  172
  173
  174
  175
  176
  177
  178
  179
  180
  181
  182
  183
  184
  185
  186
  187
  188
  189
  190
  191
  192
  193
  194
  195
  196
  197
  198
  199
  200
  201
  202
  203
  204
  205
  206
  207
  208
  209
  210
  211
  212
  213
  214
  215
  216
  217
  218
  219
  220
  221
  222
  223
  224
  225
  226
  227
  228
  229
  230
  231
  232
  233
  234
  235
  236
  237
  238
  239
  240
  241
  242
  243
  244
  245
  246
  247
  248
  249
  250
  251
  252
  253
  254
  255
  256
  257
  258
  259
  260
  261
  262
  263
  264
  265
  266
  267
  268
  269
  270
  271
  272
  273
  274
  275
  276
  277
  278
  279
  280
  281
  282
  283
  284
  285
  286
  287
  288
  289
  290
  291
  292
  293
  294
  295
  296
  297
  298
  299
  300
  301
  302
  303
  304
  305
  306
  307
  308
  309
  310
  311
  312
  313
  314
  315
  316
  317
  318
  319
  320
  321
  322
  323
  324
  325
  326
  327
  328
  329
  330
  331
  332
  333
  334
  335
  336
  337
  338
  339
  340
  341
  342
  343
  344
  345
  346
  347
  348
  349
  350
  351
  352
  353
  354
  355
  356
  357
  358
  359
  360
  361
  362
  363
  364
  365
  366
  367
  368
  369
  370
  371
  372
  373
  374
  375
  376
  377
  378
  379
  380
  381
  382
  383
  384
  385
  386
  387
  388
  389
  390
  391
  392
  393
  394
  395
  396
  397
  398
  399
  400
  401
  402
  403
  404
  405
  406
  407
  408
  409
  410
  411
  412
  413
  414
  415
  416
  417
  418
  419
  420
  421
  422
  423
  424
  425
  426
  427
  428
  429
  430
  431
  432
  433
  434
  435
  436
  437
  438
  439
  440
  441
  442
  443
  444
  445
  446
  447
  448
  449
  450
  451
  452
  453
  454
  455
  456
  457
  458
  459
  460
  461
  462
  463
  464
  465
  466
  467
  468
  469
  470
  471
  472
  473
  474
  475
  476
  477
  478
  479
  480
  481
  482
  483
  484
  485
  486
  487
  488
  489
  490
  491
  492
  493
  494
  495
  496
  497
  498
  499
  500
  501
  502
  503
  504
  505
  506
  507
  508
  509
  510
  511
  512
  513
  514
  515
  516
  517
  518
  519
  520
  521
  522
  523
  524
  525
  526
  527
  528
  529
  530
  531
  532
  533
  534
  535
  536
  537
  538
  539
  540
  541
  542
  543
  544
  545
  546
  547
  548
  549
  550
  551
  552
  553
  554
  555
  556
  557
  558
  559
  560
  561
  562
  563
  564
  565
  566
  567
  568
  569
  570
  571
  572
  573
  574
  575
  576
  577
  578
  579
  580
  581
  582
  583
  584
  585
  586
  587
  588
  589
  590
  591
  592
  593
  594
  595
  596
  597
  598
  599
  600
  601
  602
  603
  604
  605
  606
  607
  608
  609
  610
  611
  612
  613
  614
  615
  616
  617
  618
  619
  620
  621
  622
  623
  624
  625
  626
  627
  628
  629
  630
  631
  632
  633
  634
  635
  636
  637
  638
  639
  640
  641
  642
  643
  644
  645
  646
  647
  648
  649
  650
  651
  652
  653
  654
  655
  656
  657
  658
  659
  660
  661
  662
  663
  664
  665
  666
  667
  668
  669
  670
  671
  672
  673
  674
  675
  676
  677
  678
  679
  680
  681
  682
  683
  684
  685
  686
  687
  688
  689
  690
  691
  692
  693
  694
  695
  696
  697
  698
  699
  700
  701
  702
  703
  704
  705
  706
  707
  708
  709
  710
  711
  712
  713
  714
  715
  716
  717
  718
  719
  720
  721
  722
  723
  724
  725
  726
  727
  728
  729
  730
  731
  732
  733
  734
  735
  736
  737
  738
  739
  740
  741
  742
  743
  744
  745
  746
  747
  748
  749
  750
  751
  752
  753
  754
  755
  756
  757
  758
  759
  760
  761
  762
  763
  764
  765
  766
  767
  768
  769
  770
  771
  772
  773
  774
  775
  776
  777
  778
  779
  780
  781
  782
  783
  784
  785
  786
  787
  788
  789
  790
  791
  792
  793
  794
  795
  796
  797
  798
  799
  800
  801
  802
  803
  804
  805
  806
  807
  808
  809
  810
  811
  812
  813
  814
  815
  816
  817
  818
  819
  820
  821
  822
  823
  824
  825
  826
  827
  828
  829
  830
  831
  832
  833
  834
  835
  836
  837
  838
  839
  840
  841
  842
  843
  844
  845
  846
  847
  848
  849
  850
  851
  852
  853
  854
  855
  856
  857
  858
  859
  860
  861
  862
  863
  864
  865
  866
  867
  868
  869
  870
  871
  872
  873
  874
  875
  876
  877
  878
  879
  880
  881
  882
  883
  884
  885
  886
  887
  888
  889
  890
  891
  892
  893
  894
  895
  896
  897
  898
  899
  900
  901
  902
  903
  904
  905
  906
  907
  908
  909
  910
  911
  912
  913
  914
  915
  916
  917
  918
  919
  920
  921
  922
  923
  924
  925
  926
  927
  928
  929
  930
  931
  932
  933
  934
  935
  936
  937
  938
  939
  940
  941
  942
  943
  944
  945
  946
  947
  948
  949
  950
  951
  952
  953
  954
  955
  956
  957
  958
  959
  960
  961
  962
  963
  964
  965
  966
  967
  968
  969
  970
  971
  972
  973
  974
  975
  976
  977
  978
  979
  980
  981
  982
  983
  984
  985
  986
  987
  988
  989
  990
  991
  992
  993
  994
  995
  996
  997
  998
  999
 1000
 1001
 1002
 1003
 1004
 1005
 1006
 1007
 1008
 1009
 1010
 1011
 1012
 1013
 1014
 1015
 1016
 1017
 1018
 1019
 1020
 1021
 1022
 1023
 1024
 1025
 1026
 1027
 1028
 1029
 1030
 1031
 1032
 1033
 1034
 1035
 1036
 1037
 1038
 1039
 1040
 1041
 1042
 1043
 1044
 1045
 1046
 1047
 1048
 1049
 1050
 1051
 1052
 1053
 1054
 1055
 1056
 1057
 1058
 1059
 1060
 1061
 1062
 1063
 1064
 1065
 1066
 1067
 1068
 1069
 1070
 1071
 1072
 1073
 1074
 1075
 1076
 1077
 1078
 1079
 1080
 1081
 1082
 1083
 1084
 1085
 1086
 1087
 1088
 1089
 1090
 1091
 1092
 1093
 1094
 1095
 1096
 1097
 1098
 1099
 1100
 1101
 1102
 1103
 1104
 1105
 1106
 1107
 1108
 1109
 1110
 1111
 1112
 1113
 1114
 1115
 1116
 1117
 1118
 1119
 1120
 1121
 1122
 1123
 1124
 1125
 1126
 1127
 1128
 1129
 1130
 1131
 1132
 1133
 1134
 1135
 1136
 1137
 1138
 1139
 1140
 1141
 1142
 1143
 1144
 1145
 1146
 1147
 1148
 1149
 1150
 1151
 1152
 1153
 1154
 1155
 1156
 1157
 1158
 1159
 1160
 1161
 1162
 1163
 1164
 1165
 1166
 1167
 1168
 1169
 1170
 1171
 1172
 1173
 1174
 1175
 1176
 1177
 1178
 1179
 1180
 1181
 1182
 1183
 1184
 1185
 1186
 1187
 1188
 1189
 1190
 1191
 1192
 1193
 1194
 1195
 1196
 1197
 1198
 1199
 1200
 1201
 1202
 1203
 1204
 1205
 1206
 1207
 1208
 1209
 1210
 1211
 1212
 1213
 1214
 1215
 1216
 1217
 1218
 1219
 1220
 1221
 1222
 1223
 1224
 1225
 1226
 1227
 1228
 1229
 1230
 1231
 1232
 1233
 1234
 1235
 1236
 1237
 1238
 1239
 1240
 1241
 1242
 1243
 1244
 1245
 1246
 1247
 1248
 1249
 1250
 1251
 1252
 1253
 1254
 1255
 1256
 1257
 1258
 1259
 1260
 1261
 1262
 1263
 1264
 1265
 1266
 1267
 1268
 1269
 1270
 1271
 1272
 1273
 1274
 1275
 1276
 1277
 1278
 1279
 1280
 1281
 1282
 1283
 1284
 1285
 1286
 1287
 1288
 1289
 1290
 1291
 1292
 1293
 1294
 1295
 1296
 1297
 1298
 1299
 1300
 1301
 1302
 1303
 1304
 1305
 1306
 1307
 1308
 1309
 1310
 1311
 1312
 1313
 1314
 1315
 1316
 1317
 1318
 1319
 1320
 1321
 1322
 1323
 1324
 1325
 1326
 1327
 1328
 1329
 1330
 1331
 1332
 1333
 1334
 1335
 1336
 1337
 1338
 1339
 1340
 1341
 1342
 1343
 1344
 1345
 1346
 1347
 1348
 1349
 1350
 1351
 1352
 1353
 1354
 1355
 1356
 1357
 1358
 1359
 1360
 1361
 1362
 1363
 1364
 1365
 1366
 1367
 1368
 1369
 1370
 1371
 1372
 1373
 1374
 1375
 1376
 1377
 1378
 1379
 1380
 1381
 1382
 1383
 1384
 1385
 1386
 1387
 1388
 1389
 1390
 1391
 1392
 1393
 1394
 1395
 1396
 1397
 1398
 1399
 1400
 1401
 1402
 1403
 1404
 1405
 1406
 1407
 1408
 1409
 1410
 1411
 1412
 1413
 1414
 1415
 1416
 1417
 1418
 1419
 1420
 1421
 1422
 1423
 1424
 1425
 1426
 1427
 1428
 1429
 1430
 1431
 1432
 1433
 1434
 1435
 1436
 1437
 1438
 1439
 1440
 1441
 1442
 1443
 1444
 1445
 1446
 1447
 1448
 1449
 1450
 1451
 1452
 1453
 1454
 1455
 1456
 1457
 1458
 1459
 1460
 1461
 1462
 1463
 1464
 1465
 1466
 1467
 1468
 1469
 1470
 1471
 1472
 1473
 1474
 1475
 1476
 1477
 1478
 1479
 1480
 1481
 1482
 1483
 1484
 1485
 1486
 1487
 1488
 1489
 1490
 1491
 1492
 1493
 1494
 1495
 1496
 1497
 1498
 1499
 1500
 1501
 1502
 1503
 1504
 1505
 1506
 1507
 1508
 1509
 1510
 1511
 1512
 1513
 1514
 1515
 1516
 1517
 1518
 1519
 1520
 1521
 1522
 1523
 1524
 1525
 1526
 1527
 1528
 1529
 1530
 1531
 1532
 1533
 1534
 1535
 1536
 1537
 1538
 1539
 1540
 1541
 1542
 1543
 1544
 1545
 1546
 1547
 1548
 1549
 1550
 1551
 1552
 1553
 1554
 1555
 1556
 1557
 1558
 1559
 1560
 1561
 1562
 1563
 1564
 1565
 1566
 1567
 1568
 1569
 1570
 1571
 1572
 1573
 1574
 1575
 1576
 1577
 1578
 1579
 1580
 1581
 1582
 1583
 1584
 1585
 1586
 1587
 1588
 1589
 1590
 1591
 1592
 1593
 1594
 1595
 1596
 1597
 1598
 1599
 1600
 1601
 1602
 1603
 1604
 1605
 1606
 1607
 1608
 1609
 1610
 1611
 1612
 1613
 1614
 1615
 1616
 1617
 1618
 1619
 1620
 1621
 1622
 1623
 1624
 1625
 1626
 1627
 1628
 1629
 1630
 1631
 1632
 1633
 1634
 1635
 1636
 1637
 1638
 1639
 1640
 1641
 1642
 1643
 1644
 1645
 1646
 1647
 1648
 1649
 1650
 1651
 1652
 1653
 1654
 1655
 1656
 1657
 1658
 1659
 1660
 1661
 1662
 1663
 1664
 1665
 1666
 1667
 1668
 1669
 1670
 1671
 1672
 1673
 1674
 1675
 1676
 1677
 1678
 1679
 1680
 1681
 1682
 1683
 1684
 1685
 1686
 1687
 1688
 1689
 1690
 1691
 1692
 1693
 1694
 1695
 1696
 1697
 1698
 1699
 1700
 1701
 1702
 1703
 1704
 1705
 1706
 1707
 1708
 1709
 1710
 1711
 1712
 1713
 1714
 1715
 1716
 1717
 1718
 1719
 1720
 1721
 1722
 1723
 1724
 1725
 1726
 1727
 1728
 1729
 1730
 1731
 1732
 1733
 1734
 1735
 1736
 1737
 1738
 1739
 1740
 1741
 1742
 1743
 1744
 1745
 1746
 1747
 1748
 1749
 1750
 1751
 1752
 1753
 1754
 1755
 1756
 1757
 1758
 1759
 1760
 1761
 1762
 1763
 1764
 1765
 1766
 1767
 1768
 1769
 1770
 1771
 1772
 1773
 1774
 1775
 1776
 1777
 1778
 1779
 1780
 1781
 1782
 1783
 1784
 1785
 1786
 1787
 1788
 1789
 1790
 1791
 1792
 1793
 1794
 1795
 1796
 1797
 1798
 1799
 1800
 1801
 1802
 1803
 1804
 1805
 1806
 1807
 1808
 1809
 1810
 1811
 1812
 1813
 1814
 1815
 1816
 1817
 1818
 1819
 1820
 1821
 1822
 1823
 1824
 1825
 1826
 1827
 1828
 1829
 1830
 1831
 1832
 1833
 1834
 1835
 1836
 1837
 1838
 1839
 1840
 1841
 1842
 1843
 1844
 1845
 1846
 1847
 1848
 1849
 1850
 1851
 1852
 1853
 1854
 1855
 1856
 1857
 1858
 1859
 1860
 1861
 1862
 1863
 1864
 1865
 1866
 1867
 1868
 1869
 1870
 1871
 1872
 1873
 1874
 1875
 1876
 1877
 1878
 1879
 1880
 1881
 1882
 1883
 1884
 1885
 1886
 1887
 1888
 1889
 1890
 1891
 1892
 1893
 1894
 1895
 1896
 1897
 1898
 1899
 1900
 1901
 1902
 1903
 1904
 1905
 1906
 1907
 1908
 1909
 1910
 1911
 1912
 1913
 1914
 1915
 1916
 1917
 1918
 1919
 1920
 1921
 1922
 1923
 1924
 1925
 1926
 1927
 1928
 1929
 1930
 1931
 1932
 1933
 1934
 1935
 1936
 1937
 1938
 1939
 1940
 1941
 1942
 1943
 1944
 1945
 1946
 1947
 1948
 1949
 1950
 1951
 1952
 1953
 1954
 1955
 1956
 1957
 1958
 1959
 1960
 1961
 1962
 1963
 1964
 1965
 1966
 1967
 1968
 1969
 1970
 1971
 1972
 1973
 1974
 1975
 1976
 1977
 1978
 1979
 1980
 1981
 1982
 1983
 1984
 1985
 1986
 1987
 1988
 1989
 1990
 1991
 1992
 1993
 1994
 1995
 1996
 1997
 1998
 1999
 2000
 2001
 2002
 2003
 2004
 2005
 2006
 2007
 2008
 2009
 2010
 2011
 2012
 2013
 2014
 2015
 2016
 2017
 2018
 2019
 2020
 2021
 2022
 2023
 2024
 2025
 2026
 2027
 2028
 2029
 2030
 2031
 2032
 2033
 2034
 2035
 2036
 2037
 2038
 2039
 2040
 2041
 2042
 2043
 2044
 2045
 2046
 2047
 2048
 2049
 2050
 2051
 2052
 2053
 2054
 2055
 2056
 2057
 2058
 2059
 2060
 2061
 2062
 2063
 2064
 2065
 2066
 2067
 2068
 2069
 2070
 2071
 2072
 2073
 2074
 2075
 2076
 2077
 2078
 2079
 2080
 2081
 2082
 2083
 2084
 2085
 2086
 2087
 2088
 2089
 2090
 2091
 2092
 2093
 2094
 2095
 2096
 2097
 2098
 2099
 2100
 2101
 2102
 2103
 2104
 2105
 2106
 2107
 2108
 2109
 2110
 2111
 2112
 2113
 2114
 2115
 2116
 2117
 2118
 2119
 2120
 2121
 2122
 2123
 2124
 2125
 2126
 2127
 2128
 2129
 2130
 2131
 2132
 2133
 2134
 2135
 2136
 2137
 2138
 2139
 2140
 2141
 2142
 2143
 2144
 2145
 2146
 2147
 2148
 2149
 2150
 2151
 2152
 2153
 2154
 2155
 2156
 2157
 2158
 2159
 2160
 2161
 2162
 2163
 2164
 2165
 2166
 2167
 2168
 2169
 2170
 2171
 2172
 2173
 2174
 2175
 2176
 2177
 2178
 2179
 2180
 2181
 2182
 2183
 2184
 2185
 2186
 2187
 2188
 2189
 2190
 2191
 2192
 2193
 2194
 2195
 2196
 2197
 2198
 2199
 2200
 2201
 2202
 2203
 2204
 2205
 2206
 2207
 2208
 2209
 2210
 2211
 2212
 2213
 2214
 2215
 2216
 2217
 2218
 2219
 2220
 2221
 2222
 2223
 2224
 2225
 2226
 2227
 2228
 2229
 2230
 2231
 2232
 2233
 2234
 2235
 2236
 2237
 2238
 2239
 2240
 2241
 2242
 2243
 2244
 2245
 2246
 2247
 2248
 2249
 2250
 2251
 2252
 2253
 2254
 2255
 2256
 2257
 2258
 2259
 2260
 2261
 2262
 2263
 2264
 2265
 2266
 2267
 2268
 2269
 2270
 2271
 2272
 2273
 2274
 2275
 2276
 2277
 2278
 2279
 2280
 2281
 2282
 2283
 2284
 2285
 2286
 2287
 2288
 2289
 2290
 2291
 2292
 2293
 2294
 2295
 2296
 2297
 2298
 2299
 2300
 2301
 2302
 2303
 2304
 2305
 2306
 2307
 2308
 2309
 2310
 2311
 2312
 2313
 2314
 2315
 2316
 2317
 2318
 2319
 2320
 2321
 2322
 2323
 2324
 2325
 2326
 2327
 2328
 2329
 2330
 2331
 2332
 2333
 2334
 2335
 2336
 2337
 2338
 2339
 2340
 2341
 2342
 2343
 2344
 2345
 2346
 2347
 2348
 2349
 2350
 2351
 2352
 2353
 2354
 2355
 2356
 2357
 2358
 2359
 2360
 2361
 2362
 2363
 2364
 2365
 2366
 2367
 2368
 2369
 2370
 2371
 2372
 2373
 2374
 2375
 2376
 2377
 2378
 2379
 2380
 2381
 2382
 2383
 2384
 2385
 2386
 2387
 2388
 2389
 2390
 2391
 2392
 2393
 2394
 2395
 2396
 2397
 2398
 2399
 2400
 2401
 2402
 2403
 2404
 2405
 2406
 2407
 2408
 2409
 2410
 2411
 2412
 2413
 2414
 2415
 2416
 2417
 2418
 2419
 2420
 2421
 2422
 2423
 2424
 2425
 2426
 2427
 2428
 2429
 2430
 2431
 2432
 2433
 2434
 2435
 2436
 2437
 2438
 2439
 2440
 2441
 2442
 2443
 2444
 2445
 2446
 2447
 2448
 2449
 2450
 2451
 2452
 2453
 2454
 2455
 2456
 2457
 2458
 2459
 2460
 2461
 2462
 2463
 2464
 2465
 2466
 2467
 2468
 2469
 2470
 2471
 2472
 2473
 2474
 2475
 2476
 2477
 2478
 2479
 2480
 2481
 2482
 2483
 2484
 2485
 2486
 2487
 2488
 2489
 2490
 2491
 2492
 2493
 2494
 2495
 2496
 2497
 2498
 2499
 2500
 2501
 2502
 2503
 2504
 2505
 2506
 2507
 2508
 2509
 2510
 2511
 2512
 2513
 2514
 2515
 2516
 2517
 2518
 2519
 2520
 2521
 2522
 2523
 2524
 2525
 2526
 2527
 2528
 2529
 2530
 2531
 2532
 2533
 2534
 2535
 2536
 2537
 2538
 2539
 2540
 2541
 2542
 2543
 2544
 2545
 2546
 2547
 2548
 2549
 2550
 2551
 2552
 2553
 2554
 2555
 2556
 2557
 2558
 2559
 2560
 2561
 2562
 2563
 2564
 2565
 2566
 2567
 2568
 2569
 2570
 2571
 2572
 2573
 2574
 2575
 2576
 2577
 2578
 2579
 2580
 2581
 2582
 2583
 2584
 2585
 2586
 2587
 2588
 2589
 2590
 2591
 2592
 2593
 2594
 2595
 2596
 2597
 2598
 2599
 2600
 2601
 2602
 2603
 2604
 2605
 2606
 2607
 2608
 2609
 2610
 2611
 2612
 2613
 2614
 2615
 2616
 2617
 2618
 2619
 2620
 2621
 2622
 2623
 2624
 2625
 2626
 2627
 2628
 2629
 2630
 2631
 2632
 2633
 2634
 2635
 2636
 2637
 2638
 2639
 2640
 2641
 2642
 2643
 2644
 2645
 2646
 2647
 2648
 2649
 2650
 2651
 2652
 2653
 2654
 2655
 2656
 2657
 2658
 2659
 2660
 2661
 2662
 2663
 2664
 2665
 2666
 2667
 2668
 2669
 2670
 2671
 2672
 2673
 2674
 2675
 2676
 2677
 2678
 2679
 2680
 2681
 2682
 2683
 2684
 2685
 2686
 2687
 2688
 2689
 2690
 2691
 2692
 2693
 2694
 2695
 2696
 2697
 2698
 2699
 2700
 2701
 2702
 2703
 2704
 2705
 2706
 2707
 2708
 2709
 2710
 2711
 2712
 2713
 2714
 2715
 2716
 2717
 2718
 2719
 2720
 2721
 2722
 2723
 2724
 2725
 2726
 2727
 2728
 2729
 2730
 2731
 2732
 2733
 2734
 2735
 2736
 2737
 2738
 2739
 2740
 2741
 2742
 2743
 2744
 2745
 2746
 2747
 2748
 2749
 2750
 2751
 2752
 2753
 2754
 2755
 2756
 2757
 2758
 2759
 2760
 2761
 2762
 2763
 2764
 2765
 2766
 2767
 2768
 2769
 2770
 2771
 2772
 2773
 2774
 2775
 2776
 2777
 2778
 2779
 2780
 2781
 2782
 2783
 2784
 2785
 2786
 2787
 2788
 2789
 2790
 2791
 2792
 2793
 2794
 2795
 2796
 2797
 2798
 2799
 2800
 2801
 2802
 2803
 2804
 2805
 2806
 2807
 2808
 2809
 2810
 2811
 2812
 2813
 2814
 2815
 2816
 2817
 2818
 2819
 2820
 2821
 2822
 2823
 2824
 2825
 2826
 2827
 2828
 2829
 2830
 2831
 2832
 2833
 2834
 2835
 2836
 2837
 2838
 2839
 2840
 2841
 2842
 2843
 2844
 2845
 2846
 2847
 2848
 2849
 2850
 2851
 2852
 2853
 2854
 2855
 2856
 2857
 2858
 2859
 2860
 2861
 2862
 2863
 2864
 2865
 2866
 2867
 2868
 2869
 2870
 2871
 2872
 2873
 2874
 2875
 2876
 2877
 2878
 2879
 2880
 2881
 2882
 2883
 2884
 2885
 2886
 2887
 2888
 2889
 2890
 2891
 2892
 2893
 2894
 2895
 2896
 2897
 2898
 2899
 2900
 2901
 2902
 2903
 2904
 2905
 2906
 2907
 2908
 2909
 2910
 2911
 2912
 2913
 2914
 2915
 2916
 2917
 2918
 2919
 2920
 2921
 2922
 2923
 2924
 2925
 2926
 2927
 2928
 2929
 2930
 2931
 2932
 2933
 2934
 2935
 2936
 2937
 2938
 2939
 2940
 2941
 2942
 2943
 2944
 2945
 2946
 2947
 2948
 2949
 2950
 2951
 2952
 2953
 2954
 2955
 2956
 2957
 2958
 2959
 2960
 2961
 2962
 2963
 2964
 2965
 2966
 2967
 2968
 2969
 2970
 2971
 2972
 2973
 2974
 2975
 2976
 2977
 2978
 2979
 2980
 2981
 2982
 2983
 2984
 2985
 2986
 2987
 2988
 2989
 2990
 2991
 2992
 2993
 2994
 2995
 2996
 2997
 2998
 2999
 3000
 3001
 3002
 3003
 3004
 3005
 3006
 3007
 3008
 3009
 3010
 3011
 3012
 3013
 3014
 3015
 3016
 3017
 3018
 3019
 3020
 3021
 3022
 3023
 3024
 3025
 3026
 3027
 3028
 3029
 3030
 3031
 3032
 3033
 3034
 3035
 3036
 3037
 3038
 3039
 3040
 3041
 3042
 3043
 3044
 3045
 3046
 3047
 3048
 3049
 3050
 3051
 3052
 3053
 3054
 3055
 3056
 3057
 3058
 3059
 3060
 3061
 3062
 3063
 3064
 3065
 3066
 3067
 3068
 3069
 3070
 3071
 3072
 3073
 3074
 3075
 3076
 3077
 3078
 3079
 3080
 3081
 3082
 3083
 3084
 3085
 3086
 3087
 3088
 3089
 3090
 3091
 3092
 3093
 3094
 3095
 3096
 3097
 3098
 3099
 3100
 3101
 3102
 3103
 3104
 3105
 3106
 3107
 3108
 3109
 3110
 3111
 3112
 3113
 3114
 3115
 3116
 3117
 3118
 3119
 3120
 3121
 3122
 3123
 3124
 3125
 3126
 3127
 3128
 3129
 3130
 3131
 3132
 3133
 3134
 3135
 3136
 3137
 3138
 3139
 3140
 3141
 3142
 3143
 3144
 3145
 3146
 3147
 3148
 3149
 3150
 3151
 3152
 3153
 3154
 3155
 3156
 3157
 3158
 3159
 3160
 3161
 3162
 3163
 3164
 3165
 3166
 3167
 3168
 3169
 3170
 3171
 3172
 3173
 3174
 3175
 3176
 3177
 3178
 3179
 3180
 3181
 3182
 3183
 3184
 3185
 3186
 3187
 3188
 3189
 3190
 3191
 3192
 3193
 3194
 3195
 3196
 3197
 3198
 3199
 3200
 3201
 3202
 3203
 3204
 3205
 3206
 3207
 3208
 3209
 3210
 3211
 3212
 3213
 3214
 3215
 3216
 3217
 3218
 3219
 3220
 3221
 3222
 3223
 3224
 3225
 3226
 3227
 3228
 3229
 3230
 3231
 3232
 3233
 3234
 3235
 3236
 3237
 3238
 3239
 3240
 3241
 3242
 3243
 3244
 3245
 3246
 3247
 3248
 3249
 3250
 3251
 3252
 3253
 3254
 3255
 3256
 3257
 3258
 3259
 3260
 3261
 3262
 3263
 3264
 3265
 3266
 3267
 3268
 3269
 3270
 3271
 3272
 3273
 3274
 3275
 3276
 3277
 3278
 3279
 3280
 3281
 3282
 3283
 3284
 3285
 3286
 3287
 3288
 3289
 3290
 3291
 3292
 3293
 3294
 3295
 3296
 3297
 3298
 3299
 3300
 3301
 3302
 3303
 3304
 3305
 3306
 3307
 3308
 3309
 3310
 3311
 3312
 3313
 3314
 3315
 3316
 3317
 3318
 3319
 3320
 3321
 3322
 3323
 3324
 3325
 3326
 3327
 3328
 3329
 3330
 3331
 3332
 3333
 3334
 3335
 3336
 3337
 3338
 3339
 3340
 3341
 3342
 3343
 3344
 3345
 3346
 3347
 3348
 3349
 3350
 3351
 3352
 3353
 3354
 3355
 3356
 3357
 3358
 3359
 3360
 3361
 3362
 3363
 3364
 3365
 3366
 3367
 3368
 3369
 3370
 3371
 3372
 3373
 3374
 3375
 3376
 3377
 3378
 3379
 3380
 3381
 3382
 3383
 3384
 3385
 3386
 3387
 3388
 3389
 3390
 3391
 3392
 3393
 3394
 3395
 3396
 3397
 3398
 3399
 3400
 3401
 3402
 3403
 3404
 3405
 3406
 3407
 3408
 3409
 3410
 3411
 3412
 3413
 3414
 3415
 3416
 3417
 3418
 3419
 3420
 3421
 3422
 3423
 3424
 3425
 3426
 3427
 3428
 3429
 3430
 3431
 3432
 3433
 3434
 3435
 3436
 3437
 3438
 3439
 3440
 3441
 3442
 3443
 3444
 3445
 3446
 3447
 3448
 3449
 3450
 3451
 3452
 3453
 3454
 3455
 3456
 3457
 3458
 3459
 3460
 3461
 3462
 3463
 3464
 3465
 3466
 3467
 3468
 3469
 3470
 3471
 3472
 3473
 3474
 3475
 3476
 3477
 3478
 3479
 3480
 3481
 3482
 3483
 3484
 3485
 3486
 3487
 3488
 3489
 3490
 3491
 3492
 3493
 3494
 3495
 3496
 3497
 3498
 3499
 3500
 3501
 3502
 3503
 3504
 3505
 3506
 3507
 3508
 3509
 3510
 3511
 3512
 3513
 3514
 3515
 3516
 3517
 3518
 3519
 3520
 3521
 3522
 3523
 3524
 3525
 3526
 3527
 3528
 3529
 3530
 3531
 3532
 3533
 3534
 3535
 3536
 3537
 3538
 3539
 3540
 3541
 3542
 3543
 3544
 3545
 3546
 3547
 3548
 3549
 3550
 3551
 3552
 3553
 3554
 3555
 3556
 3557
 3558
 3559
 3560
 3561
 3562
 3563
 3564
 3565
 3566
 3567
 3568
 3569
 3570
 3571
 3572
 3573
 3574
 3575
 3576
 3577
 3578
 3579
 3580
 3581
 3582
 3583
 3584
 3585
 3586
 3587
 3588
 3589
 3590
 3591
 3592
 3593
 3594
 3595
 3596
 3597
 3598
 3599
 3600
 3601
 3602
 3603
 3604
 3605
 3606
 3607
 3608
 3609
 3610
 3611
 3612
 3613
 3614
 3615
 3616
 3617
 3618
 3619
 3620
 3621
 3622
 3623
 3624
 3625
 3626
 3627
 3628
 3629
 3630
 3631
 3632
 3633
 3634
 3635
 3636
 3637
 3638
 3639
 3640
 3641
 3642
 3643
 3644
 3645
 3646
 3647
 3648
 3649
 3650
 3651
 3652
 3653
 3654
 3655
 3656
 3657
 3658
 3659
 3660
 3661
 3662
 3663
 3664
 3665
 3666
 3667
 3668
 3669
 3670
 3671
 3672
 3673
 3674
 3675
 3676
 3677
 3678
 3679
 3680
 3681
 3682
 3683
 3684
 3685
 3686
 3687
 3688
 3689
 3690
 3691
 3692
 3693
 3694
 3695
 3696
 3697
 3698
 3699
 3700
 3701
 3702
 3703
 3704
 3705
 3706
 3707
 3708
 3709
 3710
 3711
 3712
 3713
 3714
 3715
 3716
 3717
 3718
 3719
 3720
 3721
 3722
 3723
 3724
 3725
 3726
 3727
 3728
 3729
 3730
 3731
 3732
 3733
 3734
 3735
 3736
 3737
 3738
 3739
 3740
 3741
 3742
 3743
 3744
 3745
 3746
 3747
 3748
 3749
 3750
 3751
 3752
 3753
 3754
 3755
 3756
 3757
 3758
 3759
 3760
 3761
 3762
 3763
 3764
 3765
 3766
 3767
 3768
 3769
 3770
 3771
 3772
 3773
 3774
 3775
 3776
 3777
 3778
 3779
 3780
 3781
 3782
 3783
 3784
 3785
 3786
 3787
 3788
 3789
 3790
 3791
 3792
 3793
 3794
 3795
 3796
 3797
 3798
 3799
 3800
 3801
 3802
 3803
 3804
 3805
 3806
 3807
 3808
 3809
 3810
 3811
 3812
 3813
 3814
 3815
 3816
 3817
 3818
 3819
 3820
 3821
 3822
 3823
 3824
 3825
 3826
 3827
 3828
 3829
 3830
 3831
 3832
 3833
 3834
 3835
 3836
 3837
 3838
 3839
 3840
 3841
 3842
 3843
 3844
 3845
 3846
 3847
 3848
 3849
 3850
 3851
 3852
 3853
 3854
 3855
 3856
 3857
 3858
 3859
 3860
 3861
 3862
 3863
 3864
 3865
 3866
 3867
 3868
 3869
 3870
 3871
 3872
 3873
 3874
 3875
 3876
 3877
 3878
 3879
 3880
 3881
 3882
 3883
 3884
 3885
 3886
 3887
 3888
 3889
 3890
 3891
 3892
 3893
 3894
 3895
 3896
 3897
 3898
 3899
 3900
 3901
 3902
 3903
 3904
 3905
 3906
 3907
 3908
 3909
 3910
 3911
 3912
 3913
 3914
 3915
 3916
 3917
 3918
 3919
 3920
 3921
 3922
 3923
 3924
 3925
 3926
 3927
 3928
 3929
 3930
 3931
 3932
 3933
 3934
 3935
 3936
 3937
 3938
 3939
 3940
 3941
 3942
 3943
 3944
 3945
 3946
 3947
 3948
 3949
 3950
 3951
 3952
 3953
 3954
 3955
 3956
 3957
 3958
 3959
 3960
 3961
 3962
 3963
 3964
 3965
 3966
 3967
 3968
 3969
 3970
 3971
 3972
 3973
 3974
 3975
 3976
 3977
 3978
 3979
 3980
 3981
 3982
 3983
 3984
 3985
 3986
 3987
 3988
 3989
 3990
 3991
 3992
 3993
 3994
 3995
 3996
 3997
 3998
 3999
 4000
 4001
 4002
 4003
 4004
 4005
 4006
 4007
 4008
 4009
 4010
 4011
 4012
 4013
 4014
 4015
 4016
 4017
 4018
 4019
 4020
 4021
 4022
 4023
 4024
 4025
 4026
 4027
 4028
 4029
 4030
 4031
 4032
 4033
 4034
 4035
 4036
 4037
 4038
 4039
 4040
 4041
 4042
 4043
 4044
 4045
 4046
 4047
 4048
 4049
 4050
 4051
 4052
 4053
 4054
 4055
 4056
 4057
 4058
 4059
 4060
 4061
 4062
 4063
 4064
 4065
 4066
 4067
 4068
 4069
 4070
 4071
 4072
 4073
 4074
 4075
 4076
 4077
 4078
 4079
 4080
 4081
 4082
 4083
 4084
 4085
 4086
 4087
 4088
 4089
 4090
 4091
 4092
 4093
 4094
 4095
 4096
 4097
 4098
 4099
 4100
 4101
 4102
 4103
 4104
 4105
 4106
 4107
 4108
 4109
 4110
 4111
 4112
 4113
 4114
 4115
 4116
 4117
 4118
 4119
 4120
 4121
 4122
 4123
 4124
 4125
 4126
 4127
 4128
 4129
 4130
 4131
 4132
 4133
 4134
 4135
 4136
 4137
 4138
 4139
 4140
 4141
 4142
 4143
 4144
 4145
 4146
 4147
 4148
 4149
 4150
 4151
 4152
 4153
 4154
 4155
 4156
 4157
 4158
 4159
 4160
 4161
 4162
 4163
 4164
 4165
 4166
 4167
 4168
 4169
 4170
 4171
 4172
 4173
 4174
 4175
 4176
 4177
 4178
 4179
 4180
 4181
 4182
 4183
 4184
 4185
 4186
 4187
 4188
 4189
 4190
 4191
 4192
 4193
 4194
 4195
 4196
 4197
 4198
 4199
 4200
 4201
 4202
 4203
 4204
 4205
 4206
 4207
 4208
 4209
 4210
 4211
 4212
 4213
 4214
 4215
 4216
 4217
 4218
 4219
 4220
 4221
 4222
 4223
 4224
 4225
 4226
 4227
 4228
 4229
 4230
 4231
 4232
 4233
 4234
 4235
 4236
 4237
 4238
 4239
 4240
 4241
 4242
 4243
 4244
 4245
 4246
 4247
 4248
 4249
 4250
 4251
 4252
 4253
 4254
 4255
 4256
 4257
 4258
 4259
 4260
 4261
 4262
 4263
 4264
 4265
 4266
 4267
 4268
 4269
 4270
 4271
 4272
 4273
 4274
 4275
 4276
 4277
 4278
 4279
 4280
 4281
 4282
 4283
 4284
 4285
 4286
 4287
 4288
 4289
 4290
 4291
 4292
 4293
 4294
 4295
 4296
 4297
 4298
 4299
 4300
 4301
 4302
 4303
 4304
 4305
 4306
 4307
 4308
 4309
 4310
 4311
 4312
 4313
 4314
 4315
 4316
 4317
 4318
 4319
 4320
 4321
 4322
 4323
 4324
 4325
 4326
 4327
 4328
 4329
 4330
 4331
 4332
 4333
 4334
 4335
 4336
 4337
 4338
 4339
 4340
 4341
 4342
 4343
 4344
 4345
 4346
 4347
 4348
 4349
 4350
 4351
 4352
 4353
 4354
 4355
 4356
 4357
 4358
 4359
 4360
 4361
 4362
 4363
 4364
 4365
 4366
 4367
 4368
 4369
 4370
 4371
 4372
 4373
 4374
 4375
 4376
 4377
 4378
 4379
 4380
 4381
 4382
 4383
 4384
 4385
 4386
 4387
 4388
 4389
 4390
 4391
 4392
 4393
 4394
 4395
 4396
 4397
 4398
 4399
 4400
 4401
 4402
 4403
 4404
 4405
 4406
 4407
 4408
 4409
 4410
 4411
 4412
 4413
 4414
 4415
 4416
 4417
 4418
 4419
 4420
 4421
 4422
 4423
 4424
 4425
 4426
 4427
 4428
 4429
 4430
 4431
 4432
 4433
 4434
 4435
 4436
 4437
 4438
 4439
 4440
 4441
 4442
 4443
 4444
 4445
 4446
 4447
 4448
 4449
 4450
 4451
 4452
 4453
 4454
 4455
 4456
 4457
 4458
 4459
 4460
 4461
 4462
 4463
 4464
 4465
 4466
 4467
 4468
 4469
 4470
 4471
 4472
 4473
 4474
 4475
 4476
 4477
 4478
 4479
 4480
 4481
 4482
 4483
 4484
 4485
 4486
 4487
 4488
 4489
 4490
 4491
 4492
 4493
 4494
 4495
 4496
 4497
 4498
 4499
 4500
 4501
 4502
 4503
 4504
 4505
 4506
 4507
 4508
 4509
 4510
 4511
 4512
 4513
 4514
 4515
 4516
 4517
 4518
 4519
 4520
 4521
 4522
 4523
 4524
 4525
 4526
 4527
 4528
 4529
 4530
 4531
 4532
 4533
 4534
 4535
 4536
 4537
 4538
 4539
 4540
 4541
 4542
 4543
 4544
 4545
 4546
 4547
 4548
 4549
 4550
 4551
 4552
 4553
 4554
 4555
 4556
 4557
 4558
 4559
 4560
 4561
 4562
 4563
 4564
 4565
 4566
 4567
 4568
 4569
 4570
 4571
 4572
 4573
 4574
 4575
 4576
 4577
 4578
 4579
 4580
 4581
 4582
 4583
 4584
 4585
 4586
 4587
 4588
 4589
 4590
 4591
 4592
 4593
 4594
 4595
 4596
 4597
 4598
 4599
 4600
 4601
 4602
 4603
 4604
 4605
 4606
 4607
 4608
 4609
 4610
 4611
 4612
 4613
 4614
 4615
 4616
 4617
 4618
 4619
 4620
 4621
 4622
 4623
 4624
 4625
 4626
 4627
 4628
 4629
 4630
 4631
 4632
 4633
 4634
 4635
 4636
 4637
 4638
 4639
 4640
 4641
 4642
 4643
 4644
 4645
 4646
 4647
 4648
 4649
 4650
 4651
 4652
 4653
 4654
 4655
 4656
 4657
 4658
 4659
 4660
 4661
 4662
 4663
 4664
 4665
 4666
 4667
 4668
 4669
 4670
 4671
 4672
 4673
 4674
 4675
 4676
 4677
 4678
 4679
 4680
 4681
 4682
 4683
 4684
 4685
 4686
 4687
 4688
 4689
 4690
 4691
 4692
 4693
 4694
 4695
 4696
 4697
 4698
 4699
 4700
 4701
 4702
 4703
 4704
 4705
 4706
 4707
 4708
 4709
 4710
 4711
 4712
 4713
 4714
 4715
 4716
 4717
 4718
 4719
 4720
 4721
 4722
 4723
 4724
 4725
 4726
 4727
 4728
 4729
 4730
 4731
 4732
 4733
 4734
 4735
 4736
 4737
 4738
 4739
 4740
 4741
 4742
 4743
 4744
 4745
 4746
 4747
 4748
 4749
 4750
 4751
 4752
 4753
 4754
 4755
 4756
 4757
 4758
 4759
 4760
 4761
 4762
 4763
 4764
 4765
 4766
 4767
 4768
 4769
 4770
 4771
 4772
 4773
 4774
 4775
 4776
 4777
 4778
 4779
 4780
 4781
 4782
 4783
 4784
 4785
 4786
 4787
 4788
 4789
 4790
 4791
 4792
 4793
 4794
 4795
 4796
 4797
 4798
 4799
 4800
 4801
 4802
 4803
 4804
 4805
 4806
 4807
 4808
 4809
 4810
 4811
 4812
 4813
 4814
 4815
 4816
 4817
 4818
 4819
 4820
 4821
 4822
 4823
 4824
 4825
 4826
 4827
 4828
 4829
 4830
 4831
 4832
 4833
 4834
 4835
 4836
 4837
 4838
 4839
 4840
 4841
 4842
 4843
 4844
 4845
 4846
 4847
 4848
 4849
 4850
 4851
 4852
 4853
 4854
 4855
 4856
 4857
 4858
 4859
 4860
 4861
 4862
 4863
 4864
 4865
 4866
 4867
 4868
 4869
 4870
 4871
 4872
 4873
 4874
 4875
 4876
 4877
 4878
 4879
 4880
 4881
 4882
 4883
 4884
 4885
 4886
 4887
 4888
 4889
 4890
 4891
 4892
 4893
 4894
 4895
 4896
 4897
 4898
 4899
 4900
 4901
 4902
 4903
 4904
 4905
 4906
 4907
 4908
 4909
 4910
 4911
 4912
 4913
 4914
 4915
 4916
 4917
 4918
 4919
 4920
 4921
 4922
 4923
 4924
 4925
 4926
 4927
 4928
 4929
 4930
 4931
 4932
 4933
 4934
 4935
 4936
 4937
 4938
 4939
 4940
 4941
 4942
 4943
 4944
 4945
 4946
 4947
 4948
 4949
 4950
 4951
 4952
 4953
 4954
 4955
 4956
 4957
 4958
 4959
 4960
 4961
 4962
 4963
 4964
 4965
 4966
 4967
 4968
 4969
 4970
 4971
 4972
 4973
 4974
 4975
 4976
 4977
 4978
 4979
 4980
 4981
 4982
 4983
 4984
 4985
 4986
 4987
 4988
 4989
 4990
 4991
 4992
 4993
 4994
 4995
 4996
 4997
 4998
 4999
 5000
 5001
 5002
 5003
 5004
 5005
 5006
 5007
 5008
 5009
 5010
 5011
 5012
 5013
 5014
 5015
 5016
 5017
 5018
 5019
 5020
 5021
 5022
 5023
 5024
 5025
 5026
 5027
 5028
 5029
 5030
 5031
 5032
 5033
 5034
 5035
 5036
 5037
 5038
 5039
 5040
 5041
 5042
 5043
 5044
 5045
 5046
 5047
 5048
 5049
 5050
 5051
 5052
 5053
 5054
 5055
 5056
 5057
 5058
 5059
 5060
 5061
 5062
 5063
 5064
 5065
 5066
 5067
 5068
 5069
 5070
 5071
 5072
 5073
 5074
 5075
 5076
 5077
 5078
 5079
 5080
 5081
 5082
 5083
 5084
 5085
 5086
 5087
 5088
 5089
 5090
 5091
 5092
 5093
 5094
 5095
 5096
 5097
 5098
 5099
 5100
 5101
 5102
 5103
 5104
 5105
 5106
 5107
 5108
 5109
 5110
 5111
 5112
 5113
 5114
 5115
 5116
 5117
 5118
 5119
 5120
 5121
 5122
 5123
 5124
 5125
 5126
 5127
 5128
 5129
 5130
 5131
 5132
 5133
 5134
 5135
 5136
 5137
 5138
 5139
 5140
 5141
 5142
 5143
 5144
 5145
 5146
 5147
 5148
 5149
 5150
 5151
 5152
 5153
 5154
 5155
 5156
 5157
 5158
 5159
 5160
 5161
 5162
 5163
 5164
 5165
 5166
 5167
 5168
 5169
 5170
 5171
 5172
 5173
 5174
 5175
 5176
 5177
 5178
 5179
 5180
 5181
 5182
 5183
 5184
 5185
 5186
 5187
 5188
 5189
 5190
 5191
 5192
 5193
 5194
 5195
 5196
 5197
 5198
 5199
 5200
 5201
 5202
 5203
 5204
 5205
 5206
 5207
 5208
 5209
 5210
 5211
 5212
 5213
 5214
 5215
 5216
 5217
 5218
 5219
 5220
 5221
 5222
 5223
 5224
 5225
 5226
 5227
 5228
 5229
 5230
 5231
 5232
 5233
 5234
 5235
 5236
 5237
 5238
 5239
 5240
 5241
 5242
 5243
 5244
 5245
 5246
 5247
 5248
 5249
 5250
 5251
 5252
 5253
 5254
 5255
 5256
 5257
 5258
 5259
 5260
 5261
 5262
 5263
 5264
 5265
 5266
 5267
 5268
 5269
 5270
 5271
 5272
 5273
 5274
 5275
 5276
 5277
 5278
 5279
 5280
 5281
 5282
 5283
 5284
 5285
 5286
 5287
 5288
 5289
 5290
 5291
 5292
 5293
 5294
 5295
 5296
 5297
 5298
 5299
 5300
 5301
 5302
 5303
 5304
 5305
 5306
 5307
 5308
 5309
 5310
 5311
 5312
 5313
 5314
 5315
 5316
 5317
 5318
 5319
 5320
 5321
 5322
 5323
 5324
 5325
 5326
 5327
 5328
 5329
 5330
 5331
 5332
 5333
 5334
 5335
 5336
 5337
 5338
 5339
 5340
 5341
 5342
 5343
 5344
 5345
 5346
 5347
 5348
 5349
 5350
 5351
 5352
 5353
 5354
 5355
 5356
 5357
 5358
 5359
 5360
 5361
 5362
 5363
 5364
 5365
 5366
 5367
 5368
 5369
 5370
 5371
 5372
 5373
 5374
 5375
 5376
 5377
 5378
 5379
 5380
 5381
 5382
 5383
 5384
 5385
 5386
 5387
 5388
 5389
 5390
 5391
 5392
 5393
 5394
 5395
 5396
 5397
 5398
 5399
 5400
 5401
 5402
 5403
 5404
 5405
 5406
 5407
 5408
 5409
 5410
 5411
 5412
 5413
 5414
 5415
 5416
 5417
 5418
 5419
 5420
 5421
 5422
 5423
 5424
 5425
 5426
 5427
 5428
 5429
 5430
 5431
 5432
 5433
 5434
 5435
 5436
 5437
 5438
 5439
 5440
 5441
 5442
 5443
 5444
 5445
 5446
 5447
 5448
 5449
 5450
 5451
 5452
 5453
 5454
 5455
 5456
 5457
 5458
 5459
 5460
 5461
 5462
 5463
 5464
 5465
 5466
 5467
 5468
 5469
 5470
 5471
 5472
 5473
 5474
 5475
 5476
 5477
 5478
 5479
 5480
 5481
 5482
 5483
 5484
 5485
 5486
 5487
 5488
 5489
 5490
 5491
 5492
 5493
 5494
 5495
 5496
 5497
 5498
 5499
 5500
 5501
 5502
 5503
 5504
 5505
 5506
 5507
 5508
 5509
 5510
 5511
 5512
 5513
 5514
 5515
 5516
 5517
 5518
 5519
 5520
 5521
 5522
 5523
 5524
 5525
 5526
 5527
 5528
 5529
 5530
 5531
 5532
 5533
 5534
 5535
 5536
 5537
 5538
 5539
 5540
 5541
 5542
 5543
 5544
 5545
 5546
 5547
 5548
 5549
 5550
 5551
 5552
 5553
 5554
 5555
 5556
 5557
 5558
 5559
 5560
 5561
 5562
 5563
 5564
 5565
 5566
 5567
 5568
 5569
 5570
 5571
 5572
 5573
 5574
 5575
 5576
 5577
 5578
 5579
 5580
 5581
 5582
 5583
 5584
 5585
 5586
 5587
 5588
 5589
 5590
 5591
 5592
 5593
 5594
 5595
 5596
 5597
 5598
 5599
 5600
 5601
 5602
 5603
 5604
 5605
 5606
 5607
 5608
 5609
 5610
 5611
 5612
 5613
 5614
 5615
 5616
 5617
 5618
 5619
 5620
 5621
 5622
 5623
 5624
 5625
 5626
 5627
 5628
 5629
 5630
 5631
 5632
 5633
 5634
 5635
 5636
 5637
 5638
 5639
 5640
 5641
 5642
 5643
 5644
 5645
 5646
 5647
 5648
 5649
 5650
 5651
 5652
 5653
 5654
 5655
 5656
 5657
 5658
 5659
 5660
 5661
 5662
 5663
 5664
 5665
 5666
 5667
 5668
 5669
 5670
 5671
 5672
 5673
 5674
 5675
 5676
 5677
 5678
 5679
 5680
 5681
 5682
 5683
 5684
 5685
 5686
 5687
 5688
 5689
 5690
 5691
 5692
 5693
 5694
 5695
 5696
 5697
 5698
 5699
 5700
 5701
 5702
 5703
 5704
 5705
 5706
 5707
 5708
 5709
 5710
 5711
 5712
 5713
 5714
 5715
 5716
 5717
 5718
 5719
 5720
 5721
 5722
 5723
 5724
 5725
 5726
 5727
 5728
 5729
 5730
 5731
 5732
 5733
 5734
 5735
 5736
 5737
 5738
 5739
 5740
 5741
 5742
 5743
 5744
 5745
 5746
 5747
 5748
 5749
 5750
 5751
 5752
 5753
 5754
 5755
 5756
 5757
 5758
 5759
 5760
 5761
 5762
 5763
 5764
 5765
 5766
 5767
 5768
 5769
 5770
 5771
 5772
 5773
 5774
 5775
 5776
 5777
 5778
 5779
 5780
 5781
 5782
 5783
 5784
 5785
 5786
 5787
 5788
 5789
 5790
 5791
 5792
 5793
 5794
 5795
 5796
 5797
 5798
 5799
 5800
 5801
 5802
 5803
 5804
 5805
 5806
 5807
 5808
 5809
 5810
 5811
 5812
 5813
 5814
 5815
 5816
 5817
 5818
 5819
 5820
 5821
 5822
 5823
 5824
 5825
 5826
 5827
 5828
 5829
 5830
 5831
 5832
 5833
 5834
 5835
 5836
 5837
 5838
 5839
 5840
 5841
 5842
 5843
 5844
 5845
 5846
 5847
 5848
 5849
 5850
 5851
 5852
 5853
 5854
 5855
 5856
 5857
 5858
 5859
 5860
 5861
 5862
 5863
 5864
 5865
 5866
 5867
 5868
 5869
 5870
 5871
 5872
 5873
 5874
 5875
 5876
 5877
 5878
 5879
 5880
 5881
 5882
 5883
 5884
 5885
 5886
 5887
 5888
 5889
 5890
 5891
 5892
 5893
 5894
 5895
 5896
 5897
 5898
 5899
 5900
 5901
 5902
 5903
 5904
 5905
 5906
 5907
 5908
 5909
 5910
 5911
 5912
 5913
 5914
 5915
 5916
 5917
 5918
 5919
 5920
 5921
 5922
 5923
 5924
 5925
 5926
 5927
 5928
 5929
 5930
 5931
 5932
 5933
 5934
 5935
 5936
 5937
 5938
 5939
 5940
 5941
 5942
 5943
 5944
 5945
 5946
 5947
 5948
 5949
 5950
 5951
 5952
 5953
 5954
 5955
 5956
 5957
 5958
 5959
 5960
 5961
 5962
 5963
 5964
 5965
 5966
 5967
 5968
 5969
 5970
 5971
 5972
 5973
 5974
 5975
 5976
 5977
 5978
 5979
 5980
 5981
 5982
 5983
 5984
 5985
 5986
 5987
 5988
 5989
 5990
 5991
 5992
 5993
 5994
 5995
 5996
 5997
 5998
 5999
 6000
 6001
 6002
 6003
 6004
 6005
 6006
 6007
 6008
 6009
 6010
 6011
 6012
 6013
 6014
 6015
 6016
 6017
 6018
 6019
 6020
 6021
 6022
 6023
 6024
 6025
 6026
 6027
 6028
 6029
 6030
 6031
 6032
 6033
 6034
 6035
 6036
 6037
 6038
 6039
 6040
 6041
 6042
 6043
 6044
 6045
 6046
 6047
 6048
 6049
 6050
 6051
 6052
 6053
 6054
 6055
 6056
 6057
 6058
 6059
 6060
 6061
 6062
 6063
 6064
 6065
 6066
 6067
 6068
 6069
 6070
 6071
 6072
 6073
 6074
 6075
 6076
 6077
 6078
 6079
 6080
 6081
 6082
 6083
 6084
 6085
 6086
 6087
 6088
 6089
 6090
 6091
 6092
 6093
 6094
 6095
 6096
 6097
 6098
 6099
 6100
 6101
 6102
 6103
 6104
 6105
 6106
 6107
 6108
 6109
 6110
 6111
 6112
 6113
 6114
 6115
 6116
 6117
 6118
 6119
 6120
 6121
 6122
 6123
 6124
 6125
 6126
 6127
 6128
 6129
 6130
 6131
 6132
 6133
 6134
 6135
 6136
 6137
 6138
 6139
 6140
 6141
 6142
 6143
 6144
 6145
 6146
 6147
 6148
 6149
 6150
 6151
 6152
 6153
 6154
 6155
 6156
 6157
 6158
 6159
 6160
 6161
 6162
 6163
 6164
 6165
 6166
 6167
 6168
 6169
 6170
 6171
 6172
 6173
 6174
 6175
 6176
 6177
 6178
 6179
 6180
 6181
 6182
 6183
 6184
 6185
 6186
 6187
 6188
 6189
 6190
 6191
 6192
 6193
 6194
 6195
 6196
 6197
 6198
 6199
 6200
 6201
 6202
 6203
 6204
 6205
 6206
 6207
 6208
 6209
 6210
 6211
 6212
 6213
 6214
 6215
 6216
 6217
 6218
 6219
 6220
 6221
 6222
 6223
 6224
 6225
 6226
 6227
 6228
 6229
 6230
 6231
 6232
 6233
 6234
 6235
 6236
 6237
 6238
 6239
 6240
 6241
 6242
 6243
 6244
 6245
 6246
 6247
 6248
 6249
 6250
 6251
 6252
 6253
 6254
 6255
 6256
 6257
 6258
 6259
 6260
 6261
 6262
 6263
 6264
 6265
 6266
 6267
 6268
 6269
 6270
 6271
 6272
 6273
 6274
 6275
 6276
 6277
 6278
 6279
 6280
 6281
 6282
 6283
 6284
 6285
 6286
 6287
 6288
 6289
 6290
 6291
 6292
 6293
 6294
 6295
 6296
 6297
 6298
 6299
 6300
 6301
 6302
 6303
 6304
 6305
 6306
 6307
 6308
 6309
 6310
 6311
 6312
 6313
 6314
 6315
 6316
 6317
 6318
 6319
 6320
 6321
 6322
 6323
 6324
 6325
 6326
 6327
 6328
 6329
 6330
 6331
 6332
 6333
 6334
 6335
 6336
 6337
 6338
 6339
 6340
 6341
 6342
 6343
 6344
 6345
 6346
 6347
 6348
 6349
 6350
 6351
 6352
 6353
 6354
 6355
 6356
 6357
 6358
 6359
 6360
 6361
 6362
 6363
 6364
 6365
 6366
 6367
 6368
 6369
 6370
 6371
 6372
 6373
 6374
 6375
 6376
 6377
 6378
 6379
 6380
 6381
 6382
 6383
 6384
 6385
 6386
 6387
 6388
 6389
 6390
 6391
 6392
 6393
 6394
 6395
 6396
 6397
 6398
 6399
 6400
 6401
 6402
 6403
 6404
 6405
 6406
 6407
 6408
 6409
 6410
 6411
 6412
 6413
 6414
 6415
 6416
 6417
 6418
 6419
 6420
 6421
 6422
 6423
 6424
 6425
 6426
 6427
 6428
 6429
 6430
 6431
 6432
 6433
 6434
 6435
 6436
 6437
 6438
 6439
 6440
 6441
 6442
 6443
 6444
 6445
 6446
 6447
 6448
 6449
 6450
 6451
 6452
 6453
 6454
 6455
 6456
 6457
 6458
 6459
 6460
 6461
 6462
 6463
 6464
 6465
 6466
 6467
 6468
 6469
 6470
 6471
 6472
 6473
 6474
 6475
 6476
 6477
 6478
 6479
 6480
 6481
 6482
 6483
 6484
 6485
 6486
 6487
 6488
 6489
 6490
 6491
 6492
 6493
 6494
 6495
 6496
 6497
 6498
 6499
 6500
 6501
 6502
 6503
 6504
 6505
 6506
 6507
 6508
 6509
 6510
 6511
 6512
 6513
 6514
 6515
 6516
 6517
 6518
 6519
 6520
 6521
 6522
 6523
 6524
 6525
 6526
 6527
 6528
 6529
 6530
 6531
 6532
 6533
 6534
 6535
 6536
 6537
 6538
 6539
 6540
 6541
 6542
 6543
 6544
 6545
 6546
 6547
 6548
 6549
 6550
 6551
 6552
 6553
 6554
 6555
 6556
 6557
 6558
 6559
 6560
 6561
 6562
 6563
 6564
 6565
 6566
 6567
 6568
 6569
 6570
 6571
 6572
 6573
 6574
 6575
 6576
 6577
 6578
 6579
 6580
 6581
 6582
 6583
 6584
 6585
 6586
 6587
 6588
 6589
 6590
 6591
 6592
 6593
 6594
 6595
 6596
 6597
 6598
 6599
 6600
 6601
 6602
 6603
 6604
 6605
 6606
 6607
 6608
 6609
 6610
 6611
 6612
 6613
 6614
 6615
 6616
 6617
 6618
 6619
 6620
 6621
 6622
 6623
 6624
 6625
 6626
 6627
 6628
 6629
 6630
 6631
 6632
 6633
 6634
 6635
 6636
 6637
 6638
 6639
 6640
 6641
 6642
 6643
 6644
 6645
 6646
 6647
 6648
 6649
 6650
 6651
 6652
 6653
 6654
 6655
 6656
 6657
 6658
 6659
 6660
 6661
 6662
 6663
 6664
 6665
 6666
 6667
 6668
 6669
 6670
 6671
 6672
 6673
 6674
 6675
 6676
 6677
 6678
 6679
 6680
 6681
 6682
 6683
 6684
 6685
 6686
 6687
 6688
 6689
 6690
 6691
 6692
 6693
 6694
 6695
 6696
 6697
 6698
 6699
 6700
 6701
 6702
 6703
 6704
 6705
 6706
 6707
 6708
 6709
 6710
 6711
 6712
 6713
 6714
 6715
 6716
 6717
 6718
 6719
 6720
 6721
 6722
 6723
 6724
 6725
 6726
 6727
 6728
 6729
 6730
 6731
 6732
 6733
 6734
 6735
 6736
 6737
 6738
 6739
 6740
 6741
 6742
 6743
 6744
 6745
 6746
 6747
 6748
 6749
 6750
 6751
 6752
 6753
 6754
 6755
 6756
 6757
 6758
 6759
 6760
 6761
 6762
 6763
 6764
 6765
 6766
 6767
 6768
 6769
 6770
 6771
 6772
 6773
 6774
 6775
 6776
 6777
 6778
 6779
 6780
 6781
 6782
 6783
 6784
 6785
 6786
 6787
 6788
 6789
 6790
 6791
 6792
 6793
 6794
 6795
 6796
 6797
 6798
 6799
 6800
 6801
 6802
 6803
 6804
 6805
 6806
 6807
 6808
 6809
 6810
 6811
 6812
 6813
 6814
 6815
 6816
 6817
 6818
 6819
 6820
 6821
 6822
 6823
 6824
 6825
 6826
 6827
 6828
 6829
 6830
 6831
 6832
 6833
 6834
 6835
 6836
 6837
 6838
 6839
 6840
 6841
 6842
 6843
 6844
 6845
 6846
 6847
 6848
 6849
 6850
 6851
 6852
 6853
 6854
 6855
 6856
 6857
 6858
 6859
 6860
 6861
 6862
 6863
 6864
 6865
 6866
 6867
 6868
 6869
 6870
 6871
 6872
 6873
 6874
 6875
 6876
 6877
 6878
 6879
 6880
 6881
 6882
 6883
 6884
 6885
 6886
 6887
 6888
 6889
 6890
 6891
 6892
 6893
 6894
 6895
 6896
 6897
 6898
 6899
 6900
 6901
 6902
 6903
 6904
 6905
 6906
 6907
 6908
 6909
 6910
 6911
 6912
 6913
 6914
 6915
 6916
 6917
 6918
 6919
 6920
 6921
 6922
 6923
 6924
 6925
 6926
 6927
 6928
 6929
 6930
 6931
 6932
 6933
 6934
 6935
 6936
 6937
 6938
 6939
 6940
 6941
 6942
 6943
 6944
 6945
 6946
 6947
 6948
 6949
 6950
 6951
 6952
 6953
 6954
 6955
 6956
 6957
 6958
 6959
 6960
 6961
 6962
 6963
 6964
 6965
 6966
 6967
 6968
 6969
 6970
 6971
 6972
 6973
 6974
 6975
 6976
 6977
 6978
 6979
 6980
 6981
 6982
 6983
 6984
 6985
 6986
 6987
 6988
 6989
 6990
 6991
 6992
 6993
 6994
 6995
 6996
 6997
 6998
 6999
 7000
 7001
 7002
 7003
 7004
 7005
 7006
 7007
 7008
 7009
 7010
 7011
 7012
 7013
 7014
 7015
 7016
 7017
 7018
 7019
 7020
 7021
 7022
 7023
 7024
 7025
 7026
 7027
 7028
 7029
 7030
 7031
 7032
 7033
 7034
 7035
 7036
 7037
 7038
 7039
 7040
 7041
 7042
 7043
 7044
 7045
 7046
 7047
 7048
 7049
 7050
 7051
 7052
 7053
 7054
 7055
 7056
 7057
 7058
 7059
 7060
 7061
 7062
 7063
 7064
 7065
 7066
 7067
 7068
 7069
 7070
 7071
 7072
 7073
 7074
 7075
 7076
 7077
 7078
 7079
 7080
 7081
 7082
 7083
 7084
 7085
 7086
 7087
 7088
 7089
 7090
 7091
 7092
 7093
 7094
 7095
 7096
 7097
 7098
 7099
 7100
 7101
 7102
 7103
 7104
 7105
 7106
 7107
 7108
 7109
 7110
 7111
 7112
 7113
 7114
 7115
 7116
 7117
 7118
 7119
 7120
 7121
 7122
 7123
 7124
 7125
 7126
 7127
 7128
 7129
 7130
 7131
 7132
 7133
 7134
 7135
 7136
 7137
 7138
 7139
 7140
 7141
 7142
 7143
 7144
 7145
 7146
 7147
 7148
 7149
 7150
 7151
 7152
 7153
 7154
 7155
 7156
 7157
 7158
 7159
 7160
 7161
 7162
 7163
 7164
 7165
 7166
 7167
 7168
 7169
 7170
 7171
 7172
 7173
 7174
 7175
 7176
 7177
 7178
 7179
 7180
 7181
 7182
 7183
 7184
 7185
 7186
 7187
 7188
 7189
 7190
 7191
 7192
 7193
 7194
 7195
 7196
 7197
 7198
 7199
 7200
 7201
 7202
 7203
 7204
 7205
 7206
 7207
 7208
 7209
 7210
 7211
 7212
 7213
 7214
 7215
 7216
 7217
 7218
 7219
 7220
 7221
 7222
 7223
 7224
 7225
 7226
 7227
 7228
 7229
 7230
 7231
 7232
 7233
 7234
 7235
 7236
 7237
 7238
 7239
 7240
 7241
 7242
 7243
 7244
 7245
 7246
 7247
 7248
 7249
 7250
 7251
 7252
 7253
 7254
 7255
 7256
 7257
 7258
 7259
 7260
 7261
 7262
 7263
 7264
 7265
 7266
 7267
 7268
 7269
 7270
 7271
 7272
 7273
 7274
 7275
 7276
 7277
 7278
 7279
 7280
 7281
 7282
 7283
 7284
 7285
 7286
 7287
 7288
 7289
 7290
 7291
 7292
 7293
 7294
 7295
 7296
 7297
 7298
 7299
 7300
 7301
 7302
 7303
 7304
 7305
 7306
 7307
 7308
 7309
 7310
 7311
 7312
 7313
 7314
 7315
 7316
 7317
 7318
 7319
 7320
 7321
 7322
 7323
 7324
 7325
 7326
 7327
 7328
 7329
 7330
 7331
 7332
 7333
 7334
 7335
 7336
 7337
 7338
 7339
 7340
 7341
 7342
 7343
 7344
 7345
 7346
 7347
 7348
 7349
 7350
 7351
 7352
 7353
 7354
 7355
 7356
 7357
 7358
 7359
 7360
 7361
 7362
 7363
 7364
 7365
 7366
 7367
 7368
 7369
 7370
 7371
 7372
 7373
 7374
 7375
 7376
 7377
 7378
 7379
 7380
 7381
 7382
 7383
 7384
 7385
 7386
 7387
 7388
 7389
 7390
 7391
 7392
 7393
 7394
 7395
 7396
 7397
 7398
 7399
 7400
 7401
 7402
 7403
 7404
 7405
 7406
 7407
 7408
 7409
 7410
 7411
 7412
 7413
 7414
 7415
 7416
 7417
 7418
 7419
 7420
 7421
 7422
 7423
 7424
 7425
 7426
 7427
 7428
 7429
 7430
 7431
 7432
 7433
 7434
 7435
 7436
 7437
 7438
 7439
 7440
 7441
 7442
 7443
 7444
 7445
 7446
 7447
 7448
 7449
 7450
 7451
 7452
 7453
 7454
 7455
 7456
 7457
 7458
 7459
 7460
 7461
 7462
 7463
 7464
 7465
 7466
 7467
 7468
 7469
 7470
 7471
 7472
 7473
 7474
 7475
 7476
 7477
 7478
 7479
 7480
 7481
 7482
 7483
 7484
 7485
 7486
 7487
 7488
 7489
 7490
 7491
 7492
 7493
 7494
 7495
 7496
 7497
 7498
 7499
 7500
 7501
 7502
 7503
 7504
 7505
 7506
 7507
 7508
 7509
 7510
 7511
 7512
 7513
 7514
 7515
 7516
 7517
 7518
 7519
 7520
 7521
 7522
 7523
 7524
 7525
 7526
 7527
 7528
 7529
 7530
 7531
 7532
 7533
 7534
 7535
 7536
 7537
 7538
 7539
 7540
 7541
 7542
 7543
 7544
 7545
 7546
 7547
 7548
 7549
 7550
 7551
 7552
 7553
 7554
 7555
 7556
 7557
 7558
 7559
 7560
 7561
 7562
 7563
 7564
 7565
 7566
 7567
 7568
 7569
 7570
 7571
 7572
 7573
 7574
 7575
 7576
 7577
 7578
 7579
 7580
 7581
 7582
 7583
 7584
 7585
 7586
 7587
 7588
 7589
 7590
 7591
 7592
 7593
 7594
 7595
 7596
 7597
 7598
 7599
 7600
 7601
 7602
 7603
 7604
 7605
 7606
 7607
 7608
 7609
 7610
 7611
 7612
 7613
 7614
 7615
 7616
 7617
 7618
 7619
 7620
 7621
 7622
 7623
 7624
 7625
 7626
 7627
 7628
 7629
 7630
 7631
 7632
 7633
 7634
 7635
 7636
 7637
 7638
 7639
 7640
 7641
 7642
 7643
 7644
 7645
 7646
 7647
 7648
 7649
 7650
 7651
 7652
 7653
 7654
 7655
 7656
 7657
 7658
 7659
 7660
 7661
 7662
 7663
 7664
 7665
 7666
 7667
 7668
 7669
 7670
 7671
 7672
 7673
 7674
 7675
 7676
 7677
 7678
 7679
 7680
 7681
 7682
 7683
 7684
 7685
 7686
 7687
 7688
 7689
 7690
 7691
 7692
 7693
 7694
 7695
 7696
 7697
 7698
 7699
 7700
 7701
 7702
 7703
 7704
 7705
 7706
 7707
 7708
 7709
 7710
 7711
 7712
 7713
 7714
 7715
 7716
 7717
 7718
 7719
 7720
 7721
 7722
 7723
 7724
 7725
 7726
 7727
 7728
 7729
 7730
 7731
 7732
 7733
 7734
 7735
 7736
 7737
 7738
 7739
 7740
 7741
 7742
 7743
 7744
 7745
 7746
 7747
 7748
 7749
 7750
 7751
 7752
 7753
 7754
 7755
 7756
 7757
 7758
 7759
 7760
 7761
 7762
 7763
 7764
 7765
 7766
 7767
 7768
 7769
 7770
 7771
 7772
 7773
 7774
 7775
 7776
 7777
 7778
 7779
 7780
 7781
 7782
 7783
 7784
 7785
 7786
 7787
 7788
 7789
 7790
 7791
 7792
 7793
 7794
 7795
 7796
 7797
 7798
 7799
 7800
 7801
 7802
 7803
 7804
 7805
 7806
 7807
 7808
 7809
 7810
 7811
 7812
 7813
 7814
 7815
 7816
 7817
 7818
 7819
 7820
 7821
 7822
 7823
 7824
 7825
 7826
 7827
 7828
 7829
 7830
 7831
 7832
 7833
 7834
 7835
 7836
 7837
 7838
 7839
 7840
 7841
 7842
 7843
 7844
 7845
 7846
 7847
 7848
 7849
 7850
 7851
 7852
 7853
 7854
 7855
 7856
 7857
 7858
 7859
 7860
 7861
 7862
 7863
 7864
 7865
 7866
 7867
 7868
 7869
 7870
 7871
 7872
 7873
 7874
 7875
 7876
 7877
 7878
 7879
 7880
 7881
 7882
 7883
 7884
 7885
 7886
 7887
 7888
 7889
 7890
 7891
 7892
 7893
 7894
 7895
 7896
 7897
 7898
 7899
 7900
 7901
 7902
 7903
 7904
 7905
 7906
 7907
 7908
 7909
 7910
 7911
 7912
 7913
 7914
 7915
 7916
 7917
 7918
 7919
 7920
 7921
 7922
 7923
 7924
 7925
 7926
 7927
 7928
 7929
 7930
 7931
 7932
 7933
 7934
 7935
 7936
 7937
 7938
 7939
 7940
 7941
 7942
 7943
 7944
 7945
 7946
 7947
 7948
 7949
 7950
 7951
 7952
 7953
 7954
 7955
 7956
 7957
 7958
 7959
 7960
 7961
 7962
 7963
 7964
 7965
 7966
 7967
 7968
 7969
 7970
 7971
 7972
 7973
 7974
 7975
 7976
 7977
 7978
 7979
 7980
 7981
 7982
 7983
 7984
 7985
 7986
 7987
 7988
 7989
 7990
 7991
 7992
 7993
 7994
 7995
 7996
 7997
 7998
 7999
 8000
 8001
 8002
 8003
 8004
 8005
 8006
 8007
 8008
 8009
 8010
 8011
 8012
 8013
 8014
 8015
 8016
 8017
 8018
 8019
 8020
 8021
 8022
 8023
 8024
 8025
 8026
 8027
 8028
 8029
 8030
 8031
 8032
 8033
 8034
 8035
 8036
 8037
 8038
 8039
 8040
 8041
 8042
 8043
 8044
 8045
 8046
 8047
 8048
 8049
 8050
 8051
 8052
 8053
 8054
 8055
 8056
 8057
 8058
 8059
 8060
 8061
 8062
 8063
 8064
 8065
 8066
 8067
 8068
 8069
 8070
 8071
 8072
 8073
 8074
 8075
 8076
 8077
 8078
 8079
 8080
 8081
 8082
 8083
 8084
 8085
 8086
 8087
 8088
 8089
 8090
 8091
 8092
 8093
 8094
 8095
 8096
 8097
 8098
 8099
 8100
 8101
 8102
 8103
 8104
 8105
 8106
 8107
 8108
 8109
 8110
 8111
 8112
 8113
 8114
 8115
 8116
 8117
 8118
 8119
 8120
 8121
 8122
 8123
 8124
 8125
 8126
 8127
 8128
 8129
 8130
 8131
 8132
 8133
 8134
 8135
 8136
 8137
 8138
 8139
 8140
 8141
 8142
 8143
 8144
 8145
 8146
 8147
 8148
 8149
 8150
 8151
 8152
 8153
 8154
 8155
 8156
 8157
 8158
 8159
 8160
 8161
 8162
 8163
 8164
 8165
 8166
 8167
 8168
 8169
 8170
 8171
 8172
 8173
 8174
 8175
 8176
 8177
 8178
 8179
 8180
 8181
 8182
 8183
 8184
 8185
 8186
 8187
 8188
 8189
 8190
 8191
 8192
 8193
 8194
 8195
 8196
 8197
 8198
 8199
 8200
 8201
 8202
 8203
 8204
 8205
 8206
 8207
 8208
 8209
 8210
 8211
 8212
 8213
 8214
 8215
 8216
 8217
 8218
 8219
 8220
 8221
 8222
 8223
 8224
 8225
 8226
 8227
 8228
 8229
 8230
 8231
 8232
 8233
 8234
 8235
 8236
 8237
 8238
 8239
 8240
 8241
 8242
 8243
 8244
 8245
 8246
 8247
 8248
 8249
 8250
 8251
 8252
 8253
 8254
 8255
 8256
 8257
 8258
 8259
 8260
 8261
 8262
 8263
 8264
 8265
 8266
 8267
 8268
 8269
 8270
 8271
 8272
 8273
 8274
 8275
 8276
 8277
 8278
 8279
 8280
 8281
 8282
 8283
 8284
 8285
 8286
 8287
 8288
 8289
 8290
 8291
 8292
 8293
 8294
 8295
 8296
 8297
 8298
 8299
 8300
 8301
 8302
 8303
 8304
 8305
 8306
 8307
 8308
 8309
 8310
 8311
 8312
 8313
 8314
 8315
 8316
 8317
 8318
 8319
 8320
 8321
 8322
 8323
 8324
 8325
 8326
 8327
 8328
 8329
 8330
 8331
 8332
 8333
 8334
 8335
 8336
 8337
 8338
 8339
 8340
 8341
 8342
 8343
 8344
 8345
 8346
 8347
 8348
 8349
 8350
 8351
 8352
 8353
 8354
 8355
 8356
 8357
 8358
 8359
 8360
 8361
 8362
 8363
 8364
 8365
 8366
 8367
 8368
 8369
 8370
 8371
 8372
 8373
 8374
 8375
 8376
 8377
 8378
 8379
 8380
 8381
 8382
 8383
 8384
 8385
 8386
 8387
 8388
 8389
 8390
 8391
 8392
 8393
 8394
 8395
 8396
 8397
 8398
 8399
 8400
 8401
 8402
 8403
 8404
 8405
 8406
 8407
 8408
 8409
 8410
 8411
 8412
 8413
 8414
 8415
 8416
 8417
 8418
 8419
 8420
 8421
 8422
 8423
 8424
 8425
 8426
 8427
 8428
 8429
 8430
 8431
 8432
 8433
 8434
 8435
 8436
 8437
 8438
 8439
 8440
 8441
 8442
 8443
 8444
 8445
 8446
 8447
 8448
 8449
 8450
 8451
 8452
 8453
 8454
 8455
 8456
 8457
 8458
 8459
 8460
 8461
 8462
 8463
 8464
 8465
 8466
 8467
 8468
 8469
 8470
 8471
 8472
 8473
 8474
 8475
 8476
 8477
 8478
 8479
 8480
 8481
 8482
 8483
 8484
 8485
 8486
 8487
 8488
 8489
 8490
 8491
 8492
 8493
 8494
 8495
 8496
 8497
 8498
 8499
 8500
 8501
 8502
 8503
 8504
 8505
 8506
 8507
 8508
 8509
 8510
 8511
 8512
 8513
 8514
 8515
 8516
 8517
 8518
 8519
 8520
 8521
 8522
 8523
 8524
 8525
 8526
 8527
 8528
 8529
 8530
 8531
 8532
 8533
 8534
 8535
 8536
 8537
 8538
 8539
 8540
 8541
 8542
 8543
 8544
 8545
 8546
 8547
 8548
 8549
 8550
 8551
 8552
 8553
 8554
 8555
 8556
 8557
 8558
 8559
 8560
 8561
 8562
 8563
 8564
 8565
 8566
 8567
 8568
 8569
 8570
 8571
 8572
 8573
 8574
 8575
 8576
 8577
 8578
 8579
 8580
 8581
 8582
 8583
 8584
 8585
 8586
 8587
 8588
 8589
 8590
 8591
 8592
 8593
 8594
 8595
 8596
 8597
 8598
 8599
 8600
 8601
 8602
 8603
 8604
 8605
 8606
 8607
 8608
 8609
 8610
 8611
 8612
 8613
 8614
 8615
 8616
 8617
 8618
 8619
 8620
 8621
 8622
 8623
 8624
 8625
 8626
 8627
 8628
 8629
 8630
 8631
 8632
 8633
 8634
 8635
 8636
 8637
 8638
 8639
 8640
 8641
 8642
 8643
 8644
 8645
 8646
 8647
 8648
 8649
 8650
 8651
 8652
 8653
 8654
 8655
 8656
 8657
 8658
 8659
 8660
 8661
 8662
 8663
 8664
 8665
 8666
 8667
 8668
 8669
 8670
 8671
 8672
 8673
 8674
 8675
 8676
 8677
 8678
 8679
 8680
 8681
 8682
 8683
 8684
 8685
 8686
 8687
 8688
 8689
 8690
 8691
 8692
 8693
 8694
 8695
 8696
 8697
 8698
 8699
 8700
 8701
 8702
 8703
 8704
 8705
 8706
 8707
 8708
 8709
 8710
 8711
 8712
 8713
 8714
 8715
 8716
 8717
 8718
 8719
 8720
 8721
 8722
 8723
 8724
 8725
 8726
 8727
 8728
 8729
 8730
 8731
 8732
 8733
 8734
 8735
 8736
 8737
 8738
 8739
 8740
 8741
 8742
 8743
 8744
 8745
 8746
 8747
 8748
 8749
 8750
 8751
 8752
 8753
 8754
 8755
 8756
 8757
 8758
 8759
 8760
 8761
 8762
 8763
 8764
 8765
 8766
 8767
 8768
 8769
 8770
 8771
 8772
 8773
 8774
 8775
 8776
 8777
 8778
 8779
 8780
 8781
 8782
 8783
 8784
 8785
 8786
 8787
 8788
 8789
 8790
 8791
 8792
 8793
 8794
 8795
 8796
 8797
 8798
 8799
 8800
 8801
 8802
 8803
 8804
 8805
 8806
 8807
 8808
 8809
 8810
 8811
 8812
 8813
 8814
 8815
 8816
 8817
 8818
 8819
 8820
 8821
 8822
 8823
 8824
 8825
 8826
 8827
 8828
 8829
 8830
 8831
 8832
 8833
 8834
 8835
 8836
 8837
 8838
 8839
 8840
 8841
 8842
 8843
 8844
 8845
 8846
 8847
 8848
 8849
 8850
 8851
 8852
 8853
 8854
 8855
 8856
 8857
 8858
 8859
 8860
 8861
 8862
 8863
 8864
 8865
 8866
 8867
 8868
 8869
 8870
 8871
 8872
 8873
 8874
 8875
 8876
 8877
 8878
 8879
 8880
 8881
 8882
 8883
 8884
 8885
 8886
 8887
 8888
 8889
 8890
 8891
 8892
 8893
 8894
 8895
 8896
 8897
 8898
 8899
 8900
 8901
 8902
 8903
 8904
 8905
 8906
 8907
 8908
 8909
 8910
 8911
 8912
 8913
 8914
 8915
 8916
 8917
 8918
 8919
 8920
 8921
 8922
 8923
 8924
 8925
 8926
 8927
 8928
 8929
 8930
 8931
 8932
 8933
 8934
 8935
 8936
 8937
 8938
 8939
 8940
 8941
 8942
 8943
 8944
 8945
 8946
 8947
 8948
 8949
 8950
 8951
 8952
 8953
 8954
 8955
 8956
 8957
 8958
 8959
 8960
 8961
 8962
 8963
 8964
 8965
 8966
 8967
 8968
 8969
 8970
 8971
 8972
 8973
 8974
 8975
 8976
 8977
 8978
 8979
 8980
 8981
 8982
 8983
 8984
 8985
 8986
 8987
 8988
 8989
 8990
 8991
 8992
 8993
 8994
 8995
 8996
 8997
 8998
 8999
 9000
 9001
 9002
 9003
 9004
 9005
 9006
 9007
 9008
 9009
 9010
 9011
 9012
 9013
 9014
 9015
 9016
 9017
 9018
 9019
 9020
 9021
 9022
 9023
 9024
 9025
 9026
 9027
 9028
 9029
 9030
 9031
 9032
 9033
 9034
 9035
 9036
 9037
 9038
 9039
 9040
 9041
 9042
 9043
 9044
 9045
 9046
 9047
 9048
 9049
 9050
 9051
 9052
 9053
 9054
 9055
 9056
 9057
 9058
 9059
 9060
 9061
 9062
 9063
 9064
 9065
 9066
 9067
 9068
 9069
 9070
 9071
 9072
 9073
 9074
 9075
 9076
 9077
 9078
 9079
 9080
 9081
 9082
 9083
 9084
 9085
 9086
 9087
 9088
 9089
 9090
 9091
 9092
 9093
 9094
 9095
 9096
 9097
 9098
 9099
 9100
 9101
 9102
 9103
 9104
 9105
 9106
 9107
 9108
 9109
 9110
 9111
 9112
 9113
 9114
 9115
 9116
 9117
 9118
 9119
 9120
 9121
 9122
 9123
 9124
 9125
 9126
 9127
 9128
 9129
 9130
 9131
 9132
 9133
 9134
 9135
 9136
 9137
 9138
 9139
 9140
 9141
 9142
 9143
 9144
 9145
 9146
 9147
 9148
 9149
 9150
 9151
 9152
 9153
 9154
 9155
 9156
 9157
 9158
 9159
 9160
 9161
 9162
 9163
 9164
 9165
 9166
 9167
 9168
 9169
 9170
 9171
 9172
 9173
 9174
 9175
 9176
 9177
 9178
 9179
 9180
 9181
 9182
 9183
 9184
 9185
 9186
 9187
 9188
 9189
 9190
 9191
 9192
 9193
 9194
 9195
 9196
 9197
 9198
 9199
 9200
 9201
 9202
 9203
 9204
 9205
 9206
 9207
 9208
 9209
 9210
 9211
 9212
 9213
 9214
 9215
 9216
 9217
 9218
 9219
 9220
 9221
 9222
 9223
 9224
 9225
 9226
 9227
 9228
 9229
 9230
 9231
 9232
 9233
 9234
 9235
 9236
 9237
 9238
 9239
 9240
 9241
 9242
 9243
 9244
 9245
 9246
 9247
 9248
 9249
 9250
 9251
 9252
 9253
 9254
 9255
 9256
 9257
 9258
 9259
 9260
 9261
 9262
 9263
 9264
 9265
 9266
 9267
 9268
 9269
 9270
 9271
 9272
 9273
 9274
 9275
 9276
 9277
 9278
 9279
 9280
 9281
 9282
 9283
 9284
 9285
 9286
 9287
 9288
 9289
 9290
 9291
 9292
 9293
 9294
 9295
 9296
 9297
 9298
 9299
 9300
 9301
 9302
 9303
 9304
 9305
 9306
 9307
 9308
 9309
 9310
 9311
 9312
 9313
 9314
 9315
 9316
 9317
 9318
 9319
 9320
 9321
 9322
 9323
 9324
 9325
 9326
 9327
 9328
 9329
 9330
 9331
 9332
 9333
 9334
 9335
 9336
 9337
 9338
 9339
 9340
 9341
 9342
 9343
 9344
 9345
 9346
 9347
 9348
 9349
 9350
 9351
 9352
 9353
 9354
 9355
 9356
 9357
 9358
 9359
 9360
 9361
 9362
 9363
 9364
 9365
 9366
 9367
 9368
 9369
 9370
 9371
 9372
 9373
 9374
 9375
 9376
 9377
 9378
 9379
 9380
 9381
 9382
 9383
 9384
 9385
 9386
 9387
 9388
 9389
 9390
 9391
 9392
 9393
 9394
 9395
 9396
 9397
 9398
 9399
 9400
 9401
 9402
 9403
 9404
 9405
 9406
 9407
 9408
 9409
 9410
 9411
 9412
 9413
 9414
 9415
 9416
 9417
 9418
 9419
 9420
 9421
 9422
 9423
 9424
 9425
 9426
 9427
 9428
 9429
 9430
 9431
 9432
 9433
 9434
 9435
 9436
 9437
 9438
 9439
 9440
 9441
 9442
 9443
 9444
 9445
 9446
 9447
 9448
 9449
 9450
 9451
 9452
 9453
 9454
 9455
 9456
 9457
 9458
 9459
 9460
 9461
 9462
 9463
 9464
 9465
 9466
 9467
 9468
 9469
 9470
 9471
 9472
 9473
 9474
 9475
 9476
 9477
 9478
 9479
 9480
 9481
 9482
 9483
 9484
 9485
 9486
 9487
 9488
 9489
 9490
 9491
 9492
 9493
 9494
 9495
 9496
 9497
 9498
 9499
 9500
 9501
 9502
 9503
 9504
 9505
 9506
 9507
 9508
 9509
 9510
 9511
 9512
 9513
 9514
 9515
 9516
 9517
 9518
 9519
 9520
 9521
 9522
 9523
 9524
 9525
 9526
 9527
 9528
 9529
 9530
 9531
 9532
 9533
 9534
 9535
 9536
 9537
 9538
 9539
 9540
 9541
 9542
 9543
 9544
 9545
 9546
 9547
 9548
 9549
 9550
 9551
 9552
 9553
 9554
 9555
 9556
 9557
 9558
 9559
 9560
 9561
 9562
 9563
 9564
 9565
 9566
 9567
 9568
 9569
 9570
 9571
 9572
 9573
 9574
 9575
 9576
 9577
 9578
 9579
 9580
 9581
 9582
 9583
 9584
 9585
 9586
 9587
 9588
 9589
 9590
 9591
 9592
 9593
 9594
 9595
 9596
 9597
 9598
 9599
 9600
 9601
 9602
 9603
 9604
 9605
 9606
 9607
 9608
 9609
 9610
 9611
 9612
 9613
 9614
 9615
 9616
 9617
 9618
 9619
 9620
 9621
 9622
 9623
 9624
 9625
 9626
 9627
 9628
 9629
 9630
 9631
 9632
 9633
 9634
 9635
 9636
 9637
 9638
 9639
 9640
 9641
 9642
 9643
 9644
 9645
 9646
 9647
 9648
 9649
 9650
 9651
 9652
 9653
 9654
 9655
 9656
 9657
 9658
 9659
 9660
 9661
 9662
 9663
 9664
 9665
 9666
 9667
 9668
 9669
 9670
 9671
 9672
 9673
 9674
 9675
 9676
 9677
 9678
 9679
 9680
 9681
 9682
 9683
 9684
 9685
 9686
 9687
 9688
 9689
 9690
 9691
 9692
 9693
 9694
 9695
 9696
 9697
 9698
 9699
 9700
 9701
 9702
 9703
 9704
 9705
 9706
 9707
 9708
 9709
 9710
 9711
 9712
 9713
 9714
 9715
 9716
 9717
 9718
 9719
 9720
 9721
 9722
 9723
 9724
 9725
 9726
 9727
 9728
 9729
 9730
 9731
 9732
 9733
 9734
 9735
 9736
 9737
 9738
 9739
 9740
 9741
 9742
 9743
 9744
 9745
 9746
 9747
 9748
 9749
 9750
 9751
 9752
 9753
 9754
 9755
 9756
 9757
 9758
 9759
 9760
 9761
 9762
 9763
 9764
 9765
 9766
 9767
 9768
 9769
 9770
 9771
 9772
 9773
 9774
 9775
 9776
 9777
 9778
 9779
 9780
 9781
 9782
 9783
 9784
 9785
 9786
 9787
 9788
 9789
 9790
 9791
 9792
 9793
 9794
 9795
 9796
 9797
 9798
 9799
 9800
 9801
 9802
 9803
 9804
 9805
 9806
 9807
 9808
 9809
 9810
 9811
 9812
 9813
 9814
 9815
 9816
 9817
 9818
 9819
 9820
 9821
 9822
 9823
 9824
 9825
 9826
 9827
 9828
 9829
 9830
 9831
 9832
 9833
 9834
 9835
 9836
 9837
 9838
 9839
 9840
 9841
 9842
 9843
 9844
 9845
 9846
 9847
 9848
 9849
 9850
 9851
 9852
 9853
 9854
 9855
 9856
 9857
 9858
 9859
 9860
 9861
 9862
 9863
 9864
 9865
 9866
 9867
 9868
 9869
 9870
 9871
 9872
 9873
 9874
 9875
 9876
 9877
 9878
 9879
 9880
 9881
 9882
 9883
 9884
 9885
 9886
 9887
 9888
 9889
 9890
 9891
 9892
 9893
 9894
 9895
 9896
 9897
 9898
 9899
 9900
 9901
 9902
 9903
 9904
 9905
 9906
 9907
 9908
 9909
 9910
 9911
 9912
 9913
 9914
 9915
 9916
 9917
 9918
 9919
 9920
 9921
 9922
 9923
 9924
 9925
 9926
 9927
 9928
 9929
 9930
 9931
 9932
 9933
 9934
 9935
 9936
 9937
 9938
 9939
 9940
 9941
 9942
 9943
 9944
 9945
 9946
 9947
 9948
 9949
 9950
 9951
 9952
 9953
 9954
 9955
 9956
 9957
 9958
 9959
 9960
 9961
 9962
 9963
 9964
 9965
 9966
 9967
 9968
 9969
 9970
 9971
 9972
 9973
 9974
 9975
 9976
 9977
 9978
 9979
 9980
 9981
 9982
 9983
 9984
 9985
 9986
 9987
 9988
 9989
 9990
 9991
 9992
 9993
 9994
 9995
 9996
 9997
 9998
 9999
10000
10001
10002
10003
10004
10005
10006
10007
10008
10009
10010
10011
10012
10013
10014
10015
10016
10017
10018
10019
10020
10021
10022
10023
10024
10025
10026
10027
10028
10029
10030
10031
10032
10033
10034
10035
10036
10037
10038
10039
10040
10041
10042
10043
10044
10045
10046
10047
10048
10049
10050
10051
10052
10053
10054
10055
10056
10057
10058
10059
10060
10061
10062
10063
10064
10065
10066
10067
10068
10069
10070
10071
10072
10073
10074
10075
10076
10077
10078
10079
10080
10081
10082
10083
10084
10085
10086
10087
10088
10089
10090
10091
10092
10093
10094
10095
10096
10097
10098
10099
10100
10101
10102
10103
10104
10105
10106
10107
10108
10109
10110
10111
10112
10113
10114
10115
10116
10117
10118
10119
10120
10121
10122
10123
10124
10125
10126
10127
10128
10129
10130
10131
10132
10133
10134
10135
10136
10137
10138
10139
10140
10141
10142
10143
10144
10145
10146
10147
10148
10149
10150
10151
10152
10153
10154
10155
10156
10157
10158
10159
10160
10161
10162
10163
10164
10165
10166
10167
10168
10169
10170
10171
10172
10173
10174
10175
10176
10177
10178
10179
10180
10181
10182
10183
10184
10185
10186
10187
10188
10189
10190
10191
10192
10193
10194
10195
10196
10197
10198
10199
10200
10201
10202
10203
10204
10205
10206
10207
10208
10209
10210
10211
10212
10213
10214
10215
10216
10217
10218
10219
10220
10221
10222
10223
10224
10225
10226
10227
10228
10229
10230
10231
10232
10233
10234
10235
10236
10237
10238
10239
10240
10241
10242
10243
10244
10245
10246
10247
10248
10249
10250
10251
10252
10253
10254
10255
10256
10257
10258
10259
10260
10261
10262
10263
10264
10265
10266
10267
10268
10269
10270
10271
10272
10273
10274
10275
10276
10277
10278
10279
10280
10281
10282
10283
10284
10285
10286
10287
10288
10289
10290
10291
10292
10293
10294
10295
10296
10297
10298
10299
10300
10301
10302
10303
10304
10305
10306
10307
10308
10309
10310
10311
10312
10313
10314
10315
10316
10317
10318
10319
10320
10321
10322
10323
10324
10325
10326
10327
10328
10329
10330
10331
10332
10333
10334
10335
10336
10337
10338
10339
10340
10341
10342
10343
10344
10345
10346
10347
10348
10349
10350
10351
10352
10353
10354
10355
10356
10357
10358
10359
10360
10361
10362
10363
10364
10365
10366
10367
10368
10369
10370
10371
10372
10373
10374
10375
10376
10377
10378
10379
10380
10381
10382
10383
10384
10385
10386
10387
10388
10389
10390
10391
10392
10393
10394
10395
10396
10397
10398
10399
10400
10401
10402
10403
10404
10405
10406
10407
10408
10409
10410
10411
10412
10413
10414
10415
10416
10417
10418
10419
10420
10421
10422
10423
10424
10425
10426
10427
10428
10429
10430
10431
10432
10433
10434
10435
10436
10437
10438
10439
10440
10441
10442
10443
10444
10445
10446
10447
10448
10449
10450
10451
10452
10453
10454
10455
10456
10457
10458
10459
10460
10461
10462
10463
10464
10465
10466
10467
10468
10469
10470
10471
10472
10473
10474
10475
10476
10477
10478
10479
10480
10481
10482
10483
10484
10485
10486
10487
10488
10489
10490
10491
10492
10493
10494
10495
10496
10497
10498
10499
10500
10501
10502
10503
10504
10505
10506
10507
10508
10509
10510
10511
10512
10513
10514
10515
10516
10517
10518
10519
10520
10521
10522
10523
10524
10525
10526
10527
10528
10529
10530
10531
10532
10533
10534
10535
10536
10537
10538
10539
10540
10541
10542
10543
10544
10545
10546
10547
10548
10549
10550
10551
10552
10553
10554
10555
10556
10557
10558
10559
10560
10561
10562
10563
10564
10565
10566
10567
10568
10569
10570
10571
10572
10573
10574
10575
10576
10577
10578
10579
10580
10581
10582
10583
10584
10585
10586
10587
10588
10589
10590
10591
10592
10593
10594
10595
10596
10597
10598
10599
10600
10601
10602
10603
10604
10605
10606
10607
10608
10609
10610
10611
10612
10613
10614
10615
10616
10617
10618
10619
10620
10621
10622
10623
10624
10625
10626
10627
10628
10629
10630
10631
10632
10633
10634
10635
10636
10637
10638
10639
10640
10641
10642
10643
10644
10645
10646
10647
10648
10649
10650
10651
10652
10653
10654
10655
10656
10657
10658
10659
10660
10661
10662
10663
10664
10665
10666
10667
10668
10669
10670
10671
10672
10673
10674
10675
10676
10677
10678
10679
10680
10681
10682
10683
10684
10685
10686
10687
10688
10689
10690
10691
10692
10693
10694
10695
10696
10697
10698
10699
10700
10701
10702
10703
10704
10705
10706
10707
10708
10709
10710
10711
10712
10713
10714
10715
10716
10717
10718
10719
10720
10721
10722
10723
10724
10725
10726
10727
10728
10729
10730
10731
10732
10733
10734
10735
10736
10737
10738
10739
10740
10741
10742
10743
10744
10745
10746
10747
10748
10749
10750
10751
10752
10753
10754
10755
10756
10757
10758
10759
10760
10761
10762
10763
10764
10765
10766
10767
10768
10769
10770
10771
10772
10773
10774
10775
10776
10777
10778
10779
10780
10781
10782
10783
10784
10785
10786
10787
10788
10789
10790
10791
10792
10793
10794
10795
10796
10797
10798
10799
10800
10801
10802
10803
10804
10805
10806
10807
10808
10809
10810
10811
10812
10813
10814
10815
10816
10817
10818
10819
10820
10821
10822
10823
10824
10825
10826
10827
10828
10829
10830
10831
10832
10833
10834
10835
10836
10837
10838
10839
10840
10841
10842
10843
10844
10845
10846
10847
10848
10849
10850
10851
10852
10853
10854
10855
10856
10857
10858
10859
10860
10861
10862
10863
10864
10865
10866
10867
10868
10869
10870
10871
10872
10873
10874
10875
10876
10877
10878
10879
10880
10881
10882
10883
10884
10885
10886
10887
10888
10889
10890
10891
10892
10893
10894
10895
10896
10897
10898
10899
10900
10901
10902
10903
10904
10905
10906
10907
10908
10909
10910
10911
10912
10913
10914
10915
10916
10917
10918
10919
10920
10921
10922
10923
10924
10925
10926
10927
10928
10929
10930
10931
10932
10933
10934
10935
10936
10937
10938
10939
10940
10941
10942
10943
10944
10945
10946
10947
10948
10949
10950
10951
10952
10953
10954
10955
10956
10957
10958
10959
10960
10961
10962
10963
10964
10965
10966
10967
10968
10969
10970
10971
10972
10973
10974
10975
10976
10977
10978
10979
10980
10981
10982
10983
10984
10985
10986
10987
10988
10989
10990
10991
10992
10993
10994
10995
10996
10997
10998
10999
11000
11001
11002
11003
11004
11005
11006
11007
11008
11009
11010
11011
11012
11013
11014
11015
11016
11017
11018
11019
11020
11021
11022
11023
11024
11025
11026
11027
11028
11029
11030
11031
11032
11033
11034
11035
11036
11037
11038
11039
11040
11041
11042
11043
11044
11045
11046
11047
11048
11049
11050
11051
11052
11053
11054
11055
11056
11057
11058
11059
11060
11061
11062
11063
11064
11065
11066
11067
11068
11069
11070
11071
11072
11073
11074
11075
11076
11077
11078
11079
11080
11081
11082
11083
11084
11085
11086
11087
11088
11089
11090
11091
11092
11093
11094
11095
11096
11097
11098
11099
11100
11101
11102
11103
11104
11105
11106
11107
11108
11109
11110
11111
11112
11113
11114
11115
11116
11117
11118
11119
11120
11121
11122
11123
11124
11125
11126
11127
11128
11129
11130
11131
11132
11133
11134
11135
11136
11137
11138
11139
11140
11141
11142
11143
11144
11145
11146
11147
11148
11149
11150
11151
11152
11153
11154
11155
11156
11157
11158
11159
11160
11161
11162
11163
11164
11165
11166
11167
11168
11169
11170
11171
11172
11173
11174
11175
11176
11177
11178
11179
11180
11181
11182
11183
11184
11185
11186
11187
11188
11189
11190
11191
11192
11193
11194
11195
11196
11197
11198
11199
11200
11201
11202
11203
11204
11205
11206
11207
11208
11209
11210
11211
11212
11213
11214
11215
11216
11217
11218
11219
11220
11221
11222
11223
11224
11225
11226
11227
11228
11229
11230
11231
11232
11233
11234
11235
11236
11237
11238
11239
11240
11241
11242
11243
11244
11245
11246
11247
11248
11249
11250
11251
11252
11253
11254
11255
11256
11257
11258
11259
11260
11261
11262
11263
11264
11265
11266
11267
11268
11269
11270
11271
11272
11273
11274
11275
11276
11277
11278
11279
11280
11281
11282
11283
11284
11285
11286
11287
11288
11289
11290
11291
11292
11293
11294
11295
11296
11297
11298
11299
11300
11301
11302
11303
11304
11305
11306
11307
11308
11309
11310
11311
11312
11313
11314
11315
11316
11317
11318
11319
11320
11321
11322
11323
11324
11325
11326
11327
11328
11329
11330
11331
11332
11333
11334
11335
11336
11337
11338
11339
11340
11341
11342
11343
11344
11345
11346
11347
11348
11349
11350
11351
11352
11353
11354
11355
11356
11357
11358
11359
11360
11361
11362
11363
11364
11365
11366
11367
11368
11369
11370
11371
11372
11373
11374
11375
11376
11377
11378
11379
11380
11381
11382
11383
11384
11385
11386
11387
11388
11389
11390
11391
11392
11393
11394
11395
11396
11397
11398
11399
11400
11401
11402
11403
11404
11405
11406
11407
11408
11409
11410
11411
11412
11413
11414
11415
11416
11417
11418
11419
11420
11421
11422
11423
11424
11425
11426
11427
11428
11429
11430
11431
11432
11433
11434
11435
11436
11437
11438
11439
11440
11441
11442
11443
11444
11445
11446
11447
11448
11449
11450
11451
11452
11453
11454
11455
11456
11457
11458
11459
11460
11461
11462
11463
11464
11465
11466
11467
11468
11469
11470
11471
11472
11473
11474
11475
11476
11477
11478
11479
11480
11481
11482
11483
11484
11485
11486
11487
11488
11489
11490
11491
11492
11493
11494
11495
11496
11497
11498
11499
11500
11501
11502
11503
11504
11505
11506
11507
11508
11509
11510
11511
11512
11513
11514
11515
11516
11517
11518
11519
11520
11521
11522
11523
11524
11525
11526
11527
11528
11529
11530
11531
11532
11533
11534
11535
11536
11537
11538
11539
11540
11541
11542
11543
11544
11545
11546
11547
11548
11549
11550
11551
11552
11553
11554
11555
11556
11557
11558
11559
11560
11561
11562
11563
11564
11565
11566
11567
11568
11569
11570
11571
11572
11573
11574
11575
11576
11577
11578
11579
11580
11581
11582
11583
11584
11585
11586
11587
11588
11589
11590
11591
11592
11593
11594
11595
11596
11597
11598
11599
11600
11601
11602
11603
11604
11605
11606
11607
11608
11609
11610
11611
11612
11613
11614
11615
11616
11617
11618
11619
11620
11621
11622
11623
11624
11625
11626
11627
11628
11629
11630
11631
11632
11633
11634
11635
11636
11637
11638
11639
11640
11641
11642
11643
11644
11645
11646
11647
11648
11649
11650
11651
11652
11653
11654
11655
11656
11657
11658
11659
11660
11661
11662
11663
11664
11665
11666
11667
11668
11669
11670
11671
11672
11673
11674
11675
11676
11677
11678
11679
11680
11681
11682
11683
11684
11685
11686
11687
11688
11689
11690
11691
11692
11693
11694
11695
11696
11697
11698
11699
11700
11701
11702
11703
11704
11705
11706
11707
11708
11709
11710
11711
11712
11713
11714
11715
11716
11717
11718
11719
11720
11721
11722
11723
11724
11725
11726
11727
11728
11729
11730
11731
11732
11733
11734
11735
11736
11737
11738
11739
11740
11741
11742
11743
11744
11745
11746
11747
11748
11749
11750
11751
11752
11753
11754
11755
11756
11757
11758
11759
11760
11761
11762
11763
11764
11765
11766
11767
11768
11769
11770
11771
11772
11773
11774
11775
11776
11777
11778
11779
11780
11781
11782
11783
11784
11785
11786
11787
11788
11789
11790
11791
11792
11793
11794
11795
11796
11797
11798
11799
11800
11801
11802
11803
11804
11805
11806
11807
11808
11809
11810
11811
11812
11813
11814
11815
11816
11817
11818
11819
11820
11821
11822
11823
11824
11825
11826
11827
11828
11829
11830
11831
11832
11833
11834
11835
11836
11837
11838
11839
11840
11841
11842
11843
11844
11845
11846
11847
11848
11849
11850
11851
11852
11853
11854
11855
11856
11857
11858
11859
11860
11861
11862
11863
11864
11865
11866
11867
11868
11869
11870
11871
11872
11873
11874
11875
11876
11877
11878
11879
11880
11881
11882
11883
11884
11885
11886
11887
11888
11889
11890
11891
11892
11893
11894
11895
11896
11897
11898
11899
11900
11901
11902
11903
11904
11905
11906
11907
11908
11909
11910
11911
11912
11913
11914
11915
11916
11917
11918
11919
11920
11921
11922
11923
11924
11925
11926
11927
11928
11929
11930
11931
11932
11933
11934
11935
11936
11937
11938
11939
11940
11941
11942
11943
11944
11945
11946
11947
11948
11949
11950
11951
11952
11953
11954
11955
11956
11957
11958
11959
11960
11961
11962
11963
11964
11965
11966
11967
11968
11969
11970
11971
11972
11973
11974
11975
11976
11977
11978
11979
11980
11981
11982
11983
11984
11985
11986
11987
11988
11989
11990
11991
11992
11993
11994
11995
11996
11997
11998
11999
12000
12001
12002
12003
12004
12005
12006
12007
12008
12009
12010
12011
12012
12013
12014
12015
12016
12017
12018
12019
12020
12021
12022
12023
12024
12025
12026
12027
12028
12029
12030
12031
12032
12033
12034
12035
12036
12037
12038
12039
12040
12041
12042
12043
12044
12045
12046
12047
12048
12049
12050
12051
12052
12053
12054
12055
12056
12057
12058
12059
12060
12061
12062
12063
12064
12065
12066
12067
12068
12069
12070
12071
12072
12073
12074
12075
12076
12077
12078
12079
12080
12081
12082
12083
12084
12085
12086
12087
12088
12089
12090
12091
12092
12093
12094
12095
12096
12097
12098
12099
12100
12101
12102
12103
12104
12105
12106
12107
12108
12109
12110
12111
12112
12113
12114
12115
12116
12117
12118
12119
12120
12121
12122
12123
12124
12125
12126
12127
12128
12129
12130
12131
12132
12133
12134
12135
12136
12137
12138
12139
12140
12141
12142
12143
12144
12145
12146
12147
12148
12149
12150
12151
12152
12153
12154
12155
12156
12157
12158
12159
12160
12161
12162
12163
12164
12165
12166
12167
12168
12169
12170
12171
12172
12173
12174
12175
12176
12177
12178
12179
12180
12181
12182
12183
12184
12185
12186
12187
12188
12189
12190
12191
12192
12193
12194
12195
12196
12197
12198
12199
12200
12201
12202
12203
12204
12205
12206
12207
12208
12209
12210
12211
12212
12213
12214
12215
12216
12217
12218
12219
12220
12221
12222
12223
12224
12225
12226
12227
12228
12229
12230
12231
12232
12233
12234
12235
12236
12237
12238
12239
12240
12241
12242
12243
12244
12245
12246
12247
12248
12249
12250
12251
12252
12253
12254
12255
12256
12257
12258
12259
12260
12261
12262
12263
12264
12265
12266
12267
12268
12269
12270
12271
12272
12273
12274
12275
12276
12277
12278
12279
12280
12281
12282
12283
12284
12285
12286
12287
12288
12289
12290
12291
12292
12293
12294
12295
12296
12297
12298
12299
12300
12301
12302
12303
12304
12305
12306
12307
12308
12309
12310
12311
12312
12313
12314
12315
12316
12317
12318
12319
12320
12321
12322
12323
12324
12325
12326
12327
12328
12329
12330
12331
12332
12333
12334
12335
12336
12337
12338
12339
12340
12341
12342
12343
12344
12345
12346
12347
12348
12349
12350
12351
12352
12353
12354
12355
12356
12357
12358
12359
12360
12361
12362
12363
12364
12365
12366
12367
12368
12369
12370
12371
12372
12373
12374
12375
12376
12377
12378
12379
12380
12381
12382
12383
12384
12385
12386
12387
12388
12389
12390
12391
12392
12393
12394
12395
12396
12397
12398
12399
12400
12401
12402
12403
12404
12405
12406
12407
12408
12409
12410
12411
12412
12413
12414
12415
12416
12417
12418
12419
12420
12421
12422
12423
12424
12425
12426
12427
12428
12429
12430
12431
12432
12433
12434
12435
12436
12437
12438
12439
12440
12441
12442
12443
12444
12445
12446
12447
12448
12449
12450
12451
12452
12453
12454
12455
12456
12457
12458
12459
12460
12461
12462
12463
12464
12465
12466
12467
12468
12469
12470
12471
12472
12473
12474
12475
12476
12477
12478
12479
12480
12481
12482
12483
12484
12485
12486
12487
12488
12489
12490
12491
12492
12493
12494
12495
12496
12497
12498
12499
12500
12501
12502
12503
12504
12505
12506
12507
12508
12509
12510
12511
12512
12513
12514
12515
12516
12517
12518
12519
12520
12521
12522
12523
12524
12525
12526
12527
12528
12529
12530
12531
12532
12533
12534
12535
12536
12537
12538
12539
12540
12541
12542
12543
12544
12545
12546
12547
12548
12549
12550
12551
12552
12553
12554
12555
12556
12557
12558
12559
12560
12561
12562
12563
12564
12565
12566
12567
12568
12569
12570
12571
12572
12573
12574
12575
12576
12577
12578
12579
12580
12581
12582
12583
12584
12585
12586
12587
12588
12589
12590
12591
12592
12593
12594
12595
12596
12597
12598
12599
12600
12601
12602
12603
12604
12605
12606
12607
12608
12609
12610
12611
12612
12613
12614
12615
12616
12617
12618
12619
12620
12621
12622
12623
12624
12625
12626
12627
12628
12629
12630
12631
12632
12633
12634
12635
12636
12637
12638
12639
12640
12641
12642
12643
12644
12645
12646
12647
12648
12649
12650
12651
12652
12653
12654
12655
12656
12657
12658
12659
12660
12661
12662
12663
12664
12665
12666
12667
12668
12669
12670
12671
12672
12673
12674
12675
12676
12677
12678
12679
12680
12681
12682
12683
12684
12685
12686
12687
12688
12689
12690
12691
12692
12693
12694
12695
12696
12697
12698
12699
12700
12701
12702
12703
12704
12705
12706
12707
12708
12709
12710
12711
12712
12713
12714
12715
12716
12717
12718
12719
12720
12721
12722
12723
12724
12725
12726
12727
12728
12729
12730
12731
12732
12733
12734
12735
12736
12737
12738
12739
12740
12741
12742
12743
12744
12745
12746
12747
12748
12749
12750
12751
12752
12753
12754
12755
12756
12757
12758
12759
12760
12761
12762
12763
12764
12765
12766
12767
12768
12769
12770
12771
12772
12773
12774
12775
12776
12777
12778
12779
12780
12781
12782
12783
12784
12785
12786
12787
12788
12789
12790
12791
12792
12793
12794
12795
12796
12797
12798
12799
12800
12801
12802
12803
12804
12805
12806
12807
12808
12809
12810
12811
12812
12813
12814
12815
12816
12817
12818
12819
12820
12821
12822
12823
12824
12825
12826
12827
12828
12829
12830
12831
12832
12833
12834
12835
12836
12837
12838
12839
12840
12841
12842
12843
12844
12845
12846
12847
12848
12849
12850
12851
12852
12853
12854
12855
12856
12857
12858
12859
12860
12861
12862
12863
12864
12865
12866
12867
12868
12869
12870
12871
12872
12873
12874
12875
12876
12877
12878
12879
12880
12881
12882
12883
12884
12885
12886
12887
12888
12889
12890
12891
12892
12893
12894
12895
12896
12897
12898
12899
12900
12901
12902
12903
12904
12905
12906
12907
12908
12909
12910
12911
12912
12913
12914
12915
12916
12917
12918
12919
12920
12921
12922
12923
12924
12925
12926
12927
12928
12929
12930
12931
12932
12933
12934
12935
12936
12937
12938
12939
12940
12941
12942
12943
12944
12945
12946
12947
12948
12949
12950
12951
12952
12953
12954
12955
12956
12957
12958
12959
12960
12961
12962
12963
12964
12965
12966
12967
12968
12969
12970
12971
12972
12973
12974
12975
12976
12977
12978
12979
12980
12981
12982
12983
12984
12985
12986
12987
12988
12989
12990
12991
12992
12993
12994
12995
12996
12997
12998
12999
13000
13001
13002
13003
13004
13005
13006
13007
13008
13009
13010
13011
13012
13013
13014
13015
13016
13017
13018
13019
13020
13021
13022
13023
13024
13025
13026
13027
13028
13029
13030
13031
13032
13033
13034
13035
13036
13037
13038
13039
13040
13041
13042
13043
13044
13045
13046
13047
13048
13049
13050
13051
13052
13053
13054
13055
13056
13057
13058
13059
13060
13061
13062
13063
13064
13065
13066
13067
13068
13069
13070
13071
13072
13073
13074
13075
13076
13077
13078
13079
13080
13081
13082
13083
13084
13085
13086
13087
13088
13089
13090
13091
13092
13093
13094
13095
13096
13097
13098
13099
13100
13101
13102
13103
13104
13105
13106
13107
13108
13109
13110
13111
13112
13113
13114
13115
13116
13117
13118
13119
13120
13121
13122
13123
13124
13125
13126
13127
13128
13129
13130
13131
13132
13133
13134
13135
13136
13137
13138
13139
13140
13141
13142
13143
13144
13145
13146
13147
13148
13149
13150
13151
13152
13153
13154
13155
13156
13157
13158
13159
13160
13161
13162
13163
13164
13165
13166
13167
13168
13169
13170
13171
13172
13173
13174
13175
13176
13177
13178
13179
13180
13181
13182
13183
13184
13185
13186
13187
13188
13189
13190
13191
13192
13193
13194
13195
13196
13197
13198
13199
13200
13201
13202
13203
13204
13205
13206
13207
13208
13209
13210
13211
13212
13213
13214
13215
13216
13217
13218
13219
13220
13221
13222
13223
13224
13225
13226
13227
13228
13229
13230
13231
13232
13233
13234
13235
13236
13237
13238
13239
13240
13241
13242
13243
13244
13245
13246
13247
13248
13249
13250
13251
13252
13253
13254
13255
13256
13257
13258
13259
13260
13261
13262
13263
13264
13265
13266
13267
13268
13269
13270
13271
13272
13273
13274
13275
13276
13277
13278
13279
13280
13281
13282
13283
13284
13285
13286
13287
13288
13289
13290
13291
13292
13293
13294
13295
13296
13297
13298
13299
13300
13301
13302
13303
13304
13305
13306
13307
13308
13309
13310
13311
13312
13313
13314
13315
13316
13317
13318
13319
13320
13321
13322
13323
13324
13325
13326
13327
13328
13329
13330
13331
13332
13333
13334
13335
13336
13337
13338
13339
13340
13341
13342
13343
13344
13345
13346
13347
13348
13349
13350
13351
13352
13353
13354
13355
13356
13357
13358
13359
13360
13361
13362
13363
13364
13365
13366
13367
13368
13369
13370
13371
13372
13373
13374
13375
13376
13377
13378
13379
13380
13381
13382
13383
13384
13385
13386
13387
13388
13389
13390
13391
13392
13393
13394
13395
13396
13397
13398
13399
13400
13401
13402
13403
13404
13405
13406
13407
13408
13409
13410
13411
13412
13413
13414
13415
13416
13417
13418
13419
13420
13421
13422
13423
13424
13425
13426
13427
13428
13429
13430
13431
13432
13433
13434
13435
13436
13437
13438
13439
13440
13441
13442
13443
13444
13445
13446
13447
13448
13449
13450
13451
13452
13453
13454
13455
13456
13457
13458
13459
13460
13461
13462
13463
13464
13465
13466
13467
13468
13469
13470
13471
13472
13473
13474
13475
13476
13477
13478
13479
13480
13481
13482
13483
13484
13485
13486
13487
13488
13489
13490
13491
13492
13493
13494
13495
13496
13497
13498
13499
13500
13501
13502
13503
13504
13505
13506
13507
13508
13509
13510
13511
13512
13513
13514
13515
13516
13517
13518
13519
13520
13521
13522
13523
13524
13525
13526
13527
13528
13529
13530
13531
13532
13533
13534
13535
13536
13537
13538
13539
13540
13541
13542
13543
13544
13545
13546
13547
13548
13549
13550
13551
13552
13553
13554
13555
13556
13557
13558
13559
13560
13561
13562
13563
13564
13565
13566
13567
13568
13569
13570
13571
13572
13573
13574
13575
13576
13577
13578
13579
13580
13581
13582
13583
13584
13585
13586
13587
13588
13589
13590
13591
13592
13593
13594
13595
13596
13597
13598
13599
13600
13601
13602
13603
13604
13605
13606
13607
13608
13609
13610
13611
13612
13613
13614
13615
13616
13617
13618
13619
13620
13621
13622
13623
13624
13625
13626
13627
13628
13629
13630
13631
13632
13633
13634
13635
13636
13637
13638
13639
13640
13641
13642
13643
13644
13645
13646
13647
13648
13649
13650
13651
13652
13653
13654
13655
13656
13657
13658
13659
13660
13661
13662
13663
13664
13665
13666
13667
13668
13669
13670
13671
13672
13673
13674
13675
13676
13677
13678
13679
13680
13681
13682
13683
13684
13685
13686
13687
13688
13689
13690
13691
13692
13693
13694
13695
13696
13697
13698
13699
13700
13701
13702
13703
13704
13705
13706
13707
13708
13709
13710
13711
13712
13713
13714
13715
13716
13717
13718
13719
13720
13721
13722
13723
13724
13725
13726
13727
13728
13729
13730
13731
13732
13733
13734
13735
13736
13737
13738
13739
13740
13741
13742
13743
13744
13745
13746
13747
13748
13749
13750
13751
13752
13753
13754
13755
13756
13757
13758
13759
13760
13761
13762
13763
13764
13765
13766
13767
13768
13769
13770
13771
13772
13773
13774
13775
13776
13777
13778
13779
13780
13781
13782
13783
13784
13785
13786
13787
13788
13789
13790
13791
13792
13793
13794
13795
13796
13797
13798
13799
13800
13801
13802
13803
13804
13805
13806
13807
13808
13809
13810
13811
13812
13813
13814
13815
13816
13817
13818
13819
13820
13821
13822
13823
13824
13825
13826
13827
13828
13829
13830
13831
13832
13833
13834
13835
13836
13837
13838
13839
13840
13841
13842
13843
13844
13845
13846
13847
13848
13849
13850
13851
13852
13853
13854
13855
13856
13857
13858
13859
13860
13861
13862
13863
13864
13865
13866
13867
13868
13869
13870
13871
13872
13873
13874
13875
13876
13877
13878
13879
13880
13881
13882
13883
13884
13885
13886
13887
13888
13889
13890
13891
13892
13893
13894
13895
13896
13897
13898
13899
13900
13901
13902
13903
13904
13905
13906
13907
13908
13909
13910
13911
13912
13913
13914
13915
13916
13917
13918
13919
13920
13921
13922
13923
13924
13925
13926
13927
13928
13929
13930
13931
13932
13933
13934
13935
13936
13937
13938
13939
13940
13941
13942
13943
13944
13945
13946
13947
13948
13949
13950
13951
13952
13953
13954
13955
13956
13957
13958
13959
13960
13961
13962
13963
13964
13965
13966
13967
13968
13969
13970
13971
13972
13973
13974
13975
13976
13977
13978
13979
13980
13981
13982
13983
13984
13985
13986
13987
13988
13989
13990
13991
13992
13993
13994
13995
13996
13997
13998
13999
14000
14001
14002
14003
14004
14005
14006
14007
14008
14009
14010
14011
14012
14013
14014
14015
14016
14017
14018
14019
14020
14021
14022
14023
14024
14025
14026
14027
14028
14029
14030
14031
14032
14033
14034
14035
14036
14037
14038
14039
14040
14041
14042
14043
14044
14045
14046
14047
14048
14049
14050
14051
14052
14053
14054
14055
14056
14057
14058
14059
14060
14061
14062
14063
14064
14065
14066
14067
14068
14069
14070
14071
14072
14073
14074
14075
14076
14077
14078
14079
14080
14081
14082
14083
14084
14085
14086
14087
14088
14089
14090
14091
14092
14093
14094
14095
14096
14097
14098
14099
14100
14101
14102
14103
14104
14105
14106
14107
14108
14109
14110
14111
14112
14113
14114
14115
14116
14117
14118
14119
14120
14121
14122
14123
14124
14125
14126
14127
14128
14129
14130
14131
14132
14133
14134
14135
14136
14137
14138
14139
14140
14141
14142
14143
14144
14145
14146
14147
14148
14149
14150
14151
14152
14153
14154
14155
14156
14157
14158
14159
14160
14161
14162
14163
14164
14165
14166
14167
14168
14169
14170
14171
14172
14173
14174
14175
14176
14177
14178
14179
14180
14181
14182
14183
14184
14185
14186
14187
14188
14189
14190
14191
14192
14193
14194
14195
14196
14197
14198
14199
14200
14201
14202
14203
14204
14205
14206
14207
14208
14209
14210
14211
14212
14213
14214
14215
14216
14217
14218
14219
14220
14221
14222
14223
14224
14225
14226
14227
14228
14229
14230
14231
14232
14233
14234
14235
14236
14237
14238
14239
14240
14241
14242
14243
14244
14245
14246
14247
14248
14249
14250
14251
14252
14253
14254
14255
14256
14257
14258
14259
14260
14261
14262
14263
14264
14265
14266
14267
14268
14269
14270
14271
14272
14273
14274
14275
14276
14277
14278
14279
14280
14281
14282
14283
14284
14285
14286
14287
14288
14289
14290
14291
14292
14293
14294
14295
14296
14297
14298
14299
14300
14301
14302
14303
14304
14305
14306
14307
14308
14309
14310
14311
14312
14313
14314
14315
14316
14317
14318
14319
14320
14321
14322
14323
14324
14325
14326
14327
14328
14329
14330
14331
14332
14333
14334
14335
14336
14337
14338
14339
14340
14341
14342
14343
14344
14345
14346
14347
14348
14349
14350
14351
14352
14353
14354
14355
14356
14357
14358
14359
14360
14361
14362
14363
14364
14365
14366
14367
14368
14369
14370
14371
14372
14373
14374
14375
14376
14377
14378
14379
14380
14381
14382
14383
14384
14385
14386
14387
14388
14389
14390
14391
14392
14393
14394
14395
14396
14397
14398
14399
14400
14401
14402
14403
14404
14405
14406
14407
14408
14409
14410
14411
14412
14413
14414
14415
14416
14417
14418
14419
14420
14421
14422
14423
14424
14425
14426
14427
14428
14429
14430
14431
14432
14433
14434
14435
14436
14437
14438
14439
14440
14441
14442
14443
14444
14445
14446
14447
14448
14449
14450
14451
14452
14453
14454
14455
14456
14457
14458
14459
14460
14461
14462
14463
14464
14465
14466
14467
14468
14469
14470
14471
14472
14473
14474
14475
14476
14477
14478
14479
14480
14481
14482
14483
14484
14485
14486
14487
14488
14489
14490
14491
14492
14493
14494
14495
14496
14497
14498
14499
14500
14501
14502
14503
14504
14505
14506
14507
14508
14509
14510
14511
14512
14513
14514
14515
14516
14517
14518
14519
14520
14521
14522
14523
14524
14525
14526
14527
14528
14529
14530
14531
14532
14533
14534
14535
14536
14537
14538
14539
14540
14541
14542
14543
14544
14545
14546
14547
14548
14549
14550
14551
14552
14553
14554
14555
14556
14557
14558
14559
14560
14561
14562
14563
14564
14565
14566
14567
14568
14569
14570
14571
14572
14573
14574
14575
14576
14577
14578
14579
14580
14581
14582
14583
14584
14585
14586
14587
14588
14589
14590
14591
14592
14593
14594
14595
14596
14597
14598
14599
14600
14601
14602
14603
14604
14605
14606
14607
14608
14609
14610
14611
14612
14613
14614
14615
14616
14617
14618
14619
14620
14621
14622
14623
14624
14625
14626
14627
14628
14629
14630
14631
14632
14633
14634
14635
14636
14637
14638
14639
14640
14641
14642
14643
14644
14645
14646
14647
14648
14649
14650
14651
14652
14653
14654
14655
14656
14657
14658
14659
14660
14661
14662
14663
14664
14665
14666
14667
14668
14669
14670
14671
14672
14673
14674
14675
14676
14677
14678
14679
14680
14681
14682
14683
14684
14685
14686
14687
14688
14689
14690
14691
14692
14693
14694
14695
14696
14697
14698
14699
14700
14701
14702
14703
14704
14705
14706
14707
14708
14709
14710
14711
14712
14713
14714
14715
14716
14717
14718
14719
14720
14721
14722
14723
14724
14725
14726
14727
14728
14729
14730
14731
14732
14733
14734
14735
14736
14737
14738
14739
14740
14741
14742
14743
14744
14745
14746
14747
14748
14749
14750
14751
14752
14753
14754
14755
14756
14757
14758
14759
14760
14761
14762
14763
14764
14765
14766
14767
14768
14769
14770
14771
14772
14773
14774
14775
14776
14777
14778
14779
14780
14781
14782
14783
14784
14785
14786
14787
14788
14789
14790
14791
14792
14793
14794
14795
14796
14797
14798
14799
14800
14801
14802
14803
14804
14805
14806
14807
14808
14809
14810
14811
14812
14813
14814
14815
14816
14817
14818
14819
14820
14821
14822
14823
14824
14825
14826
14827
14828
14829
14830
14831
14832
14833
14834
14835
14836
14837
14838
14839
14840
14841
14842
14843
14844
14845
14846
14847
14848
14849
14850
14851
14852
14853
14854
14855
14856
14857
14858
14859
14860
14861
14862
14863
14864
14865
14866
14867
14868
14869
14870
14871
14872
14873
14874
14875
14876
14877
14878
14879
14880
14881
14882
14883
14884
14885
14886
14887
14888
14889
14890
14891
14892
14893
14894
14895
14896
14897
14898
14899
14900
14901
14902
14903
14904
14905
14906
14907
14908
14909
14910
14911
14912
14913
14914
14915
14916
14917
14918
14919
14920
14921
14922
14923
14924
14925
14926
14927
14928
14929
14930
14931
14932
14933
14934
14935
14936
14937
14938
14939
14940
14941
14942
14943
14944
14945
14946
14947
14948
14949
14950
14951
14952
14953
14954
14955
14956
14957
14958
14959
14960
14961
14962
14963
14964
14965
14966
14967
14968
14969
14970
14971
14972
14973
14974
14975
14976
14977
14978
14979
14980
14981
14982
14983
14984
14985
14986
14987
14988
14989
14990
14991
14992
14993
14994
14995
14996
14997
14998
14999
15000
15001
15002
15003
15004
15005
15006
15007
15008
15009
15010
15011
15012
15013
15014
15015
15016
15017
15018
15019
15020
15021
15022
15023
15024
15025
15026
15027
15028
15029
15030
15031
15032
15033
15034
15035
15036
15037
15038
15039
15040
15041
15042
15043
15044
15045
15046
15047
15048
15049
15050
15051
15052
15053
15054
15055
15056
15057
15058
15059
15060
15061
15062
15063
15064
15065
15066
15067
15068
15069
15070
15071
15072
15073
15074
15075
15076
15077
15078
15079
15080
15081
15082
15083
15084
15085
15086
15087
15088
15089
15090
15091
15092
15093
15094
15095
15096
15097
15098
15099
15100
15101
15102
15103
15104
15105
15106
15107
15108
15109
15110
15111
15112
15113
15114
15115
15116
15117
15118
15119
15120
15121
15122
15123
15124
15125
15126
15127
15128
15129
15130
15131
15132
15133
15134
15135
15136
15137
15138
15139
15140
15141
15142
15143
15144
15145
15146
15147
15148
15149
15150
15151
15152
15153
15154
15155
15156
15157
15158
15159
15160
15161
15162
15163
15164
15165
15166
15167
15168
15169
15170
15171
15172
15173
15174
15175
15176
15177
15178
15179
15180
15181
15182
15183
15184
15185
15186
15187
15188
15189
15190
15191
15192
15193
15194
15195
15196
15197
15198
15199
15200
15201
15202
15203
15204
15205
15206
15207
15208
15209
15210
15211
15212
15213
15214
15215
15216
15217
15218
15219
15220
15221
15222
15223
15224
15225
15226
15227
15228
15229
15230
15231
15232
15233
15234
15235
15236
15237
15238
15239
15240
15241
15242
15243
15244
15245
15246
15247
15248
15249
15250
15251
15252
15253
15254
15255
15256
15257
15258
15259
15260
15261
15262
15263
15264
15265
15266
15267
15268
15269
15270
15271
15272
15273
15274
15275
15276
15277
15278
15279
15280
15281
15282
15283
15284
15285
15286
15287
15288
15289
15290
15291
15292
15293
15294
15295
15296
15297
15298
15299
15300
15301
15302
15303
15304
15305
15306
15307
15308
15309
15310
15311
15312
15313
15314
15315
15316
15317
15318
15319
15320
15321
15322
15323
15324
15325
15326
15327
15328
15329
15330
15331
15332
15333
15334
15335
15336
15337
15338
15339
15340
15341
15342
15343
15344
15345
15346
15347
15348
15349
15350
15351
15352
15353
15354
15355
15356
15357
15358
15359
15360
15361
15362
15363
15364
15365
15366
15367
15368
15369
15370
15371
15372
15373
15374
15375
15376
15377
15378
15379
15380
15381
15382
15383
15384
15385
15386
15387
15388
15389
15390
15391
15392
15393
15394
15395
15396
15397
15398
15399
15400
15401
15402
15403
15404
15405
15406
15407
15408
15409
15410
15411
15412
15413
15414
15415
15416
15417
15418
15419
15420
15421
15422
15423
15424
15425
15426
15427
15428
15429
15430
15431
15432
15433
15434
15435
15436
15437
15438
15439
15440
15441
15442
15443
15444
15445
15446
15447
15448
15449
15450
15451
15452
15453
15454
15455
15456
15457
15458
15459
15460
15461
15462
15463
15464
15465
15466
15467
15468
15469
15470
15471
15472
15473
15474
15475
15476
15477
15478
15479
15480
15481
15482
15483
15484
15485
15486
15487
15488
15489
15490
15491
15492
15493
15494
15495
15496
15497
15498
15499
15500
15501
15502
15503
15504
15505
15506
15507
15508
15509
15510
15511
15512
15513
15514
15515
15516
15517
15518
15519
15520
15521
15522
15523
15524
15525
15526
15527
15528
15529
15530
15531
15532
15533
15534
15535
15536
15537
15538
15539
15540
15541
15542
15543
15544
15545
15546
15547
15548
15549
15550
15551
15552
15553
15554
15555
15556
15557
15558
15559
15560
15561
15562
15563
15564
15565
15566
15567
15568
15569
15570
15571
15572
15573
15574
15575
15576
15577
15578
15579
15580
15581
15582
15583
15584
15585
15586
15587
15588
15589
15590
15591
15592
15593
15594
15595
15596
15597
15598
15599
15600
15601
15602
15603
15604
15605
15606
15607
15608
15609
15610
15611
15612
15613
15614
15615
15616
15617
15618
15619
15620
15621
15622
15623
15624
15625
15626
15627
15628
15629
15630
15631
15632
15633
15634
15635
15636
15637
15638
15639
15640
15641
15642
15643
15644
15645
15646
15647
15648
15649
15650
15651
15652
15653
15654
15655
15656
15657
15658
15659
15660
15661
15662
15663
15664
15665
15666
15667
15668
15669
15670
15671
15672
15673
15674
15675
15676
15677
15678
15679
15680
15681
15682
15683
15684
15685
15686
15687
15688
15689
15690
15691
15692
15693
15694
15695
15696
15697
15698
15699
15700
15701
15702
15703
15704
15705
15706
15707
15708
15709
15710
15711
15712
15713
15714
15715
15716
15717
15718
15719
15720
15721
15722
15723
15724
15725
15726
15727
15728
15729
15730
15731
15732
15733
15734
15735
15736
15737
15738
15739
15740
15741
15742
15743
15744
15745
15746
15747
15748
15749
15750
15751
15752
15753
15754
15755
15756
15757
15758
15759
15760
15761
15762
15763
15764
15765
15766
15767
15768
15769
15770
15771
15772
15773
15774
15775
15776
15777
15778
15779
15780
15781
15782
15783
15784
15785
15786
15787
15788
15789
15790
15791
15792
15793
15794
15795
15796
15797
15798
15799
15800
15801
15802
15803
15804
15805
15806
15807
15808
15809
15810
15811
15812
15813
15814
15815
15816
15817
15818
15819
15820
15821
15822
15823
15824
15825
15826
15827
15828
15829
15830
15831
15832
15833
15834
15835
15836
15837
15838
15839
15840
15841
15842
15843
15844
15845
15846
15847
15848
15849
15850
15851
15852
15853
15854
15855
15856
15857
15858
15859
15860
15861
15862
15863
15864
15865
15866
15867
15868
15869
15870
15871
15872
15873
15874
15875
15876
15877
15878
15879
15880
15881
15882
15883
15884
15885
15886
15887
15888
15889
15890
15891
15892
15893
15894
15895
15896
15897
15898
15899
15900
15901
15902
15903
15904
15905
15906
15907
15908
15909
15910
15911
15912
15913
15914
15915
15916
15917
15918
15919
15920
15921
15922
15923
15924
15925
15926
15927
15928
15929
15930
15931
15932
15933
15934
15935
15936
15937
15938
15939
15940
15941
15942
15943
15944
15945
15946
15947
15948
15949
15950
15951
15952
15953
15954
15955
15956
15957
15958
15959
15960
15961
15962
15963
15964
15965
15966
15967
15968
15969
15970
15971
15972
15973
15974
15975
15976
15977
15978
15979
15980
15981
15982
15983
15984
15985
15986
15987
15988
15989
15990
15991
15992
15993
15994
15995
15996
15997
15998
15999
16000
16001
16002
16003
16004
16005
16006
16007
16008
16009
16010
16011
16012
16013
16014
16015
16016
16017
16018
16019
16020
16021
16022
16023
16024
16025
16026
16027
16028
16029
16030
16031
16032
16033
16034
16035
16036
16037
16038
16039
16040
16041
16042
16043
16044
16045
16046
16047
16048
16049
16050
16051
16052
16053
16054
16055
16056
16057
16058
16059
16060
16061
16062
16063
16064
16065
16066
16067
16068
16069
16070
16071
16072
16073
16074
16075
16076
16077
16078
16079
16080
16081
16082
16083
16084
16085
16086
16087
16088
16089
16090
16091
16092
16093
16094
16095
16096
16097
16098
16099
16100
16101
16102
16103
16104
16105
16106
16107
16108
16109
16110
16111
16112
16113
16114
16115
16116
16117
16118
16119
16120
16121
16122
16123
16124
16125
16126
16127
16128
16129
16130
16131
16132
16133
16134
16135
16136
16137
16138
16139
16140
16141
16142
16143
16144
16145
16146
16147
16148
16149
16150
16151
16152
16153
16154
16155
16156
16157
16158
16159
16160
16161
16162
16163
16164
16165
16166
16167
16168
16169
16170
16171
16172
16173
16174
16175
16176
16177
16178
16179
16180
16181
16182
16183
16184
16185
16186
16187
16188
16189
16190
16191
16192
16193
16194
16195
16196
16197
16198
16199
16200
16201
16202
16203
16204
16205
16206
16207
16208
16209
16210
16211
16212
16213
16214
16215
16216
16217
16218
16219
16220
16221
16222
16223
16224
16225
16226
16227
16228
16229
16230
16231
16232
16233
16234
16235
16236
16237
16238
16239
16240
16241
16242
16243
16244
16245
16246
16247
16248
16249
16250
16251
16252
16253
16254
16255
16256
16257
16258
16259
16260
16261
16262
16263
16264
16265
16266
16267
16268
16269
16270
16271
16272
16273
16274
16275
16276
16277
16278
16279
16280
16281
16282
16283
16284
16285
16286
16287
16288
16289
16290
16291
16292
16293
16294
16295
16296
16297
16298
16299
16300
16301
16302
16303
16304
16305
16306
16307
16308
16309
16310
16311
16312
16313
16314
16315
16316
16317
16318
16319
16320
16321
16322
16323
16324
16325
16326
16327
16328
16329
16330
16331
16332
16333
16334
16335
16336
16337
16338
16339
16340
16341
16342
16343
16344
16345
16346
16347
16348
16349
16350
16351
16352
16353
16354
16355
16356
16357
16358
16359
16360
16361
16362
16363
16364
16365
16366
16367
16368
16369
16370
16371
16372
16373
16374
16375
16376
16377
16378
16379
16380
16381
16382
16383
16384
16385
16386
16387
16388
16389
16390
16391
16392
16393
16394
16395
16396
16397
16398
16399
16400
16401
16402
16403
16404
16405
16406
16407
16408
16409
16410
16411
16412
16413
16414
16415
16416
16417
16418
16419
16420
16421
16422
16423
16424
16425
16426
16427
16428
16429
16430
16431
16432
16433
16434
16435
16436
16437
16438
16439
16440
16441
16442
16443
16444
16445
16446
16447
16448
16449
16450
16451
16452
16453
16454
16455
16456
16457
16458
16459
16460
16461
16462
16463
16464
16465
16466
16467
16468
16469
16470
16471
16472
16473
16474
16475
16476
16477
16478
16479
16480
16481
16482
16483
16484
16485
16486
16487
16488
16489
16490
16491
16492
16493
16494
16495
16496
16497
16498
16499
16500
16501
16502
16503
16504
16505
16506
16507
16508
16509
16510
16511
16512
16513
16514
16515
16516
16517
16518
16519
16520
16521
16522
16523
16524
16525
16526
16527
16528
16529
16530
16531
16532
16533
16534
16535
16536
16537
16538
16539
16540
16541
16542
16543
16544
16545
16546
16547
16548
16549
16550
16551
16552
16553
16554
16555
16556
16557
16558
16559
16560
16561
16562
16563
16564
16565
16566
16567
16568
16569
16570
16571
16572
16573
16574
16575
16576
16577
16578
16579
16580
16581
16582
16583
16584
16585
16586
16587
16588
16589
16590
16591
16592
16593
16594
16595
16596
16597
16598
16599
16600
16601
16602
16603
16604
16605
16606
16607
16608
16609
16610
16611
16612
16613
16614
16615
16616
16617
16618
16619
16620
16621
16622
16623
16624
16625
16626
16627
16628
16629
16630
16631
16632
16633
16634
16635
16636
16637
16638
16639
16640
16641
16642
16643
16644
16645
16646
16647
16648
16649
16650
16651
16652
16653
16654
16655
16656
16657
16658
16659
16660
16661
16662
16663
16664
16665
16666
16667
16668
16669
16670
16671
16672
16673
16674
16675
16676
16677
16678
16679
16680
16681
16682
16683
16684
16685
16686
16687
16688
16689
16690
16691
16692
16693
16694
16695
16696
16697
16698
16699
16700
16701
16702
16703
16704
16705
16706
16707
16708
16709
16710
16711
16712
16713
16714
16715
16716
16717
16718
16719
16720
16721
16722
16723
16724
16725
16726
16727
16728
16729
16730
16731
16732
16733
16734
16735
16736
16737
16738
16739
16740
16741
16742
16743
16744
16745
16746
16747
16748
16749
16750
16751
16752
16753
16754
16755
16756
16757
16758
16759
16760
16761
16762
16763
16764
16765
16766
16767
16768
16769
16770
16771
16772
16773
16774
16775
16776
16777
16778
16779
16780
16781
16782
16783
16784
16785
16786
16787
16788
16789
16790
16791
16792
16793
16794
16795
16796
16797
16798
16799
16800
16801
16802
16803
16804
16805
16806
16807
16808
16809
16810
16811
16812
16813
16814
16815
16816
16817
16818
16819
16820
16821
16822
16823
16824
16825
16826
16827
16828
16829
16830
16831
16832
16833
16834
16835
16836
16837
16838
16839
16840
16841
16842
16843
16844
16845
16846
16847
16848
16849
16850
16851
16852
16853
16854
16855
16856
16857
16858
16859
16860
16861
16862
16863
16864
16865
16866
16867
16868
16869
16870
16871
16872
16873
16874
16875
16876
16877
16878
16879
16880
16881
16882
16883
16884
16885
16886
16887
16888
16889
16890
16891
16892
16893
16894
16895
16896
16897
16898
16899
16900
16901
16902
16903
16904
16905
16906
16907
16908
16909
16910
16911
16912
16913
16914
16915
16916
16917
16918
16919
16920
16921
16922
16923
16924
16925
16926
16927
16928
16929
16930
16931
16932
16933
16934
16935
16936
16937
16938
16939
16940
16941
16942
16943
16944
16945
16946
16947
16948
16949
16950
16951
16952
16953
16954
16955
16956
16957
16958
16959
16960
16961
16962
16963
16964
16965
16966
16967
16968
16969
16970
16971
16972
16973
16974
16975
16976
16977
16978
16979
16980
16981
16982
16983
16984
16985
16986
16987
16988
16989
16990
16991
16992
16993
16994
16995
16996
16997
16998
16999
17000
17001
17002
17003
17004
17005
17006
17007
17008
17009
17010
17011
17012
17013
17014
17015
17016
17017
17018
17019
17020
17021
17022
17023
17024
17025
17026
17027
17028
17029
17030
17031
17032
17033
17034
17035
17036
17037
17038
17039
17040
17041
17042
17043
17044
17045
17046
17047
17048
17049
17050
17051
17052
17053
17054
17055
17056
17057
17058
17059
17060
17061
17062
17063
17064
17065
17066
17067
17068
17069
17070
17071
17072
17073
17074
17075
17076
17077
17078
17079
17080
17081
17082
17083
17084
17085
17086
17087
17088
17089
17090
17091
17092
17093
17094
17095
17096
17097
17098
17099
17100
17101
17102
17103
17104
17105
17106
17107
17108
17109
17110
17111
17112
17113
17114
17115
17116
17117
17118
17119
17120
17121
17122
17123
17124
17125
17126
17127
17128
17129
17130
17131
17132
17133
17134
17135
17136
17137
17138
17139
17140
17141
17142
17143
17144
17145
17146
17147
17148
17149
17150
17151
17152
17153
17154
17155
17156
17157
17158
17159
17160
17161
17162
17163
17164
17165
17166
17167
17168
17169
17170
17171
17172
17173
17174
17175
17176
17177
17178
17179
17180
17181
17182
17183
17184
17185
17186
17187
17188
17189
17190
17191
17192
17193
17194
17195
17196
17197
17198
17199
17200
17201
17202
17203
17204
17205
17206
17207
17208
17209
17210
17211
17212
17213
17214
17215
17216
17217
17218
17219
17220
17221
17222
17223
17224
17225
17226
17227
17228
17229
17230
17231
17232
17233
17234
17235
17236
17237
17238
17239
17240
17241
17242
17243
17244
17245
17246
17247
17248
17249
17250
17251
17252
17253
17254
17255
17256
17257
17258
17259
17260
17261
17262
17263
17264
17265
17266
17267
17268
17269
17270
17271
17272
17273
17274
17275
17276
17277
17278
17279
17280
17281
17282
17283
17284
17285
17286
17287
17288
17289
17290
17291
17292
17293
17294
17295
17296
17297
17298
17299
17300
17301
17302
17303
17304
17305
17306
17307
17308
17309
17310
17311
17312
17313
17314
17315
17316
17317
17318
17319
17320
17321
17322
17323
17324
17325
17326
17327
17328
17329
17330
17331
17332
17333
17334
17335
17336
17337
17338
17339
17340
17341
17342
17343
17344
17345
17346
17347
17348
17349
17350
17351
17352
17353
17354
17355
17356
17357
17358
17359
17360
17361
17362
17363
17364
17365
17366
17367
17368
17369
17370
17371
17372
17373
17374
17375
17376
17377
17378
17379
17380
17381
17382
17383
17384
17385
17386
17387
17388
17389
17390
17391
17392
17393
17394
17395
17396
17397
17398
17399
17400
17401
17402
17403
17404
17405
17406
17407
17408
17409
17410
17411
17412
17413
17414
17415
17416
17417
17418
17419
17420
17421
17422
17423
17424
17425
17426
17427
17428
17429
17430
17431
17432
17433
17434
17435
17436
17437
17438
17439
17440
17441
17442
17443
17444
17445
17446
17447
17448
17449
17450
17451
17452
17453
17454
17455
17456
17457
17458
17459
17460
17461
17462
17463
17464
17465
17466
17467
17468
17469
17470
17471
17472
17473
17474
17475
17476
17477
17478
17479
17480
17481
17482
17483
17484
17485
17486
17487
17488
17489
17490
17491
17492
17493
17494
17495
17496
17497
17498
17499
17500
17501
17502
17503
17504
17505
17506
17507
17508
17509
17510
17511
17512
17513
17514
17515
17516
17517
17518
17519
17520
17521
17522
17523
17524
17525
17526
17527
17528
17529
17530
17531
17532
17533
17534
17535
17536
17537
17538
17539
17540
17541
17542
17543
17544
17545
17546
17547
17548
17549
17550
17551
17552
17553
17554
17555
17556
17557
17558
17559
17560
17561
17562
17563
17564
17565
17566
17567
17568
17569
17570
17571
17572
17573
17574
17575
17576
17577
17578
17579
17580
17581
17582
17583
17584
17585
17586
17587
17588
17589
17590
17591
17592
17593
17594
17595
17596
17597
17598
17599
17600
17601
17602
17603
17604
17605
17606
17607
17608
17609
17610
17611
17612
17613
17614
17615
17616
17617
17618
17619
17620
17621
17622
17623
17624
17625
17626
17627
17628
17629
17630
17631
17632
17633
17634
17635
17636
17637
17638
17639
17640
17641
17642
17643
17644
17645
17646
17647
17648
17649
17650
17651
17652
17653
17654
17655
17656
17657
17658
17659
17660
17661
17662
17663
17664
17665
17666
17667
17668
17669
17670
17671
17672
17673
17674
17675
17676
17677
17678
17679
17680
17681
17682
17683
17684
17685
17686
17687
17688
17689
17690
17691
17692
17693
17694
17695
17696
17697
17698
17699
17700
17701
17702
17703
17704
17705
17706
17707
17708
17709
17710
17711
17712
17713
17714
17715
17716
17717
17718
17719
17720
17721
17722
17723
17724
17725
17726
17727
17728
17729
17730
17731
17732
17733
17734
17735
17736
17737
17738
17739
17740
17741
17742
17743
17744
17745
17746
17747
17748
17749
17750
17751
17752
17753
17754
17755
17756
17757
17758
17759
17760
17761
17762
17763
17764
17765
17766
17767
17768
17769
17770
17771
17772
17773
17774
17775
17776
17777
17778
17779
17780
17781
17782
17783
17784
17785
17786
17787
17788
17789
17790
17791
17792
17793
17794
17795
17796
17797
17798
17799
17800
17801
17802
17803
17804
17805
17806
17807
17808
17809
17810
17811
17812
17813
17814
17815
17816
17817
17818
17819
17820
17821
17822
17823
17824
17825
17826
17827
17828
17829
17830
17831
17832
17833
17834
17835
17836
17837
17838
17839
17840
17841
17842
17843
17844
17845
17846
17847
17848
17849
17850
17851
17852
17853
17854
17855
17856
17857
17858
17859
17860
17861
17862
17863
17864
17865
17866
17867
17868
17869
17870
17871
17872
17873
17874
17875
17876
17877
17878
17879
17880
17881
17882
17883
17884
17885
17886
17887
17888
17889
17890
17891
17892
17893
17894
17895
17896
17897
17898
17899
17900
17901
17902
17903
17904
17905
17906
17907
17908
17909
17910
17911
17912
17913
17914
17915
17916
17917
17918
17919
17920
17921
17922
17923
17924
17925
17926
17927
17928
17929
17930
17931
17932
17933
17934
17935
17936
17937
17938
17939
17940
17941
17942
17943
17944
17945
17946
17947
17948
17949
17950
17951
17952
17953
17954
17955
17956
17957
17958
17959
17960
17961
17962
17963
17964
17965
17966
17967
17968
17969
17970
17971
17972
17973
17974
17975
17976
17977
17978
17979
17980
17981
17982
17983
17984
17985
17986
17987
17988
17989
17990
17991
17992
17993
17994
17995
17996
17997
17998
17999
18000
18001
18002
18003
18004
18005
18006
18007
18008
18009
18010
18011
18012
18013
18014
18015
18016
18017
18018
18019
18020
18021
18022
18023
18024
18025
18026
18027
18028
18029
18030
18031
18032
18033
18034
18035
18036
18037
18038
18039
18040
18041
18042
18043
18044
18045
18046
18047
18048
18049
18050
18051
18052
18053
18054
18055
18056
18057
18058
18059
18060
18061
18062
18063
18064
18065
18066
18067
18068
18069
18070
18071
18072
18073
18074
18075
18076
18077
18078
18079
18080
18081
18082
18083
18084
18085
18086
18087
18088
18089
18090
18091
18092
18093
18094
18095
18096
18097
18098
18099
18100
18101
18102
18103
18104
18105
18106
18107
18108
18109
18110
18111
18112
18113
18114
18115
18116
18117
18118
18119
18120
18121
18122
18123
18124
18125
18126
18127
18128
18129
18130
18131
18132
18133
18134
18135
18136
18137
18138
18139
18140
18141
18142
18143
18144
18145
18146
18147
18148
18149
18150
18151
18152
18153
18154
18155
18156
18157
18158
18159
18160
18161
18162
18163
18164
18165
18166
18167
18168
18169
18170
18171
18172
18173
18174
18175
18176
18177
18178
18179
18180
18181
18182
18183
18184
18185
18186
18187
18188
18189
18190
18191
18192
18193
18194
18195
18196
18197
18198
18199
18200
18201
18202
18203
18204
18205
18206
18207
18208
18209
18210
18211
18212
18213
18214
18215
18216
18217
18218
18219
18220
18221
18222
18223
18224
18225
18226
18227
18228
18229
18230
18231
18232
18233
18234
18235
18236
18237
18238
18239
18240
18241
18242
18243
18244
18245
18246
18247
18248
18249
18250
18251
18252
18253
18254
18255
18256
18257
18258
18259
18260
18261
18262
18263
18264
18265
18266
18267
18268
18269
18270
18271
18272
18273
18274
18275
18276
18277
18278
18279
18280
18281
18282
18283
18284
18285
18286
18287
18288
18289
18290
18291
18292
18293
18294
18295
18296
18297
18298
18299
18300
18301
18302
18303
18304
18305
18306
18307
18308
18309
18310
18311
18312
18313
18314
18315
18316
18317
18318
18319
18320
18321
18322
18323
18324
18325
18326
18327
18328
18329
18330
18331
18332
18333
18334
18335
18336
18337
18338
18339
18340
18341
18342
18343
18344
18345
18346
18347
18348
18349
18350
18351
18352
18353
18354
18355
18356
18357
18358
18359
18360
18361
18362
18363
18364
18365
18366
18367
18368
18369
18370
18371
18372
18373
18374
18375
18376
18377
18378
18379
18380
18381
18382
18383
18384
18385
18386
18387
18388
18389
18390
18391
18392
18393
18394
18395
18396
18397
18398
18399
18400
18401
18402
18403
18404
18405
18406
18407
18408
18409
18410
18411
18412
18413
18414
18415
18416
18417
18418
18419
18420
18421
18422
18423
18424
18425
18426
18427
18428
18429
18430
18431
18432
18433
18434
18435
18436
18437
18438
18439
18440
18441
18442
18443
18444
18445
18446
18447
18448
18449
18450
18451
18452
18453
18454
18455
18456
18457
18458
18459
18460
18461
18462
18463
18464
18465
18466
18467
18468
18469
18470
18471
18472
18473
18474
18475
18476
18477
18478
18479
18480
18481
18482
18483
18484
18485
18486
18487
18488
18489
18490
18491
18492
18493
18494
18495
18496
18497
18498
18499
18500
18501
18502
18503
18504
18505
18506
18507
18508
18509
18510
18511
18512
18513
18514
18515
18516
18517
18518
18519
18520
18521
18522
18523
18524
18525
18526
18527
18528
18529
18530
18531
18532
18533
18534
18535
18536
18537
18538
18539
18540
18541
18542
18543
18544
18545
18546
18547
18548
18549
18550
18551
18552
18553
18554
18555
18556
18557
18558
18559
18560
18561
18562
18563
18564
18565
18566
18567
18568
18569
18570
18571
18572
18573
18574
18575
18576
18577
18578
18579
18580
18581
18582
18583
18584
18585
18586
18587
18588
18589
18590
18591
18592
18593
18594
18595
18596
18597
18598
18599
18600
18601
18602
18603
18604
18605
18606
18607
18608
18609
18610
18611
18612
18613
18614
18615
18616
18617
18618
18619
18620
18621
18622
18623
18624
18625
18626
18627
18628
18629
18630
18631
18632
18633
18634
18635
18636
18637
18638
18639
18640
18641
18642
18643
18644
18645
18646
18647
18648
18649
18650
18651
18652
18653
18654
18655
18656
18657
18658
18659
18660
18661
18662
18663
18664
18665
18666
18667
18668
18669
18670
18671
18672
18673
18674
18675
18676
18677
18678
18679
18680
18681
18682
18683
18684
18685
18686
18687
18688
18689
18690
18691
18692
18693
18694
18695
18696
18697
18698
18699
18700
18701
18702
18703
18704
18705
18706
18707
18708
18709
18710
18711
18712
18713
18714
18715
18716
18717
18718
18719
18720
18721
18722
18723
18724
18725
18726
18727
18728
18729
18730
18731
18732
18733
18734
18735
18736
18737
18738
18739
18740
18741
18742
18743
18744
18745
18746
18747
18748
18749
18750
18751
18752
18753
18754
18755
18756
18757
18758
18759
18760
18761
18762
18763
18764
18765
18766
18767
18768
18769
18770
18771
18772
18773
18774
18775
18776
18777
18778
18779
18780
18781
18782
18783
18784
18785
18786
18787
18788
18789
18790
18791
18792
18793
18794
18795
18796
18797
18798
18799
18800
18801
18802
18803
18804
18805
18806
18807
18808
18809
18810
18811
18812
18813
18814
18815
18816
18817
18818
18819
18820
18821
18822
18823
18824
18825
18826
18827
18828
18829
18830
18831
18832
18833
18834
18835
18836
18837
18838
18839
18840
18841
18842
18843
18844
18845
18846
18847
18848
18849
18850
18851
18852
18853
18854
18855
18856
18857
18858
18859
18860
18861
18862
18863
18864
18865
18866
18867
18868
18869
18870
18871
18872
18873
18874
18875
18876
18877
18878
18879
18880
18881
18882
18883
18884
18885
18886
18887
18888
18889
18890
18891
18892
18893
18894
18895
18896
18897
18898
18899
18900
18901
18902
18903
18904
18905
18906
18907
18908
18909
18910
18911
18912
18913
18914
18915
18916
18917
18918
18919
18920
18921
18922
18923
18924
18925
18926
18927
18928
18929
18930
18931
18932
18933
18934
18935
18936
18937
18938
18939
18940
18941
18942
18943
18944
18945
18946
18947
18948
18949
18950
18951
18952
18953
18954
18955
18956
18957
18958
18959
18960
18961
18962
18963
18964
18965
18966
18967
18968
18969
18970
18971
18972
18973
18974
18975
18976
18977
18978
18979
18980
18981
18982
18983
18984
18985
18986
18987
18988
18989
18990
18991
18992
18993
18994
18995
18996
18997
18998
18999
19000
19001
19002
19003
19004
19005
19006
19007
19008
19009
19010
19011
19012
19013
19014
19015
19016
19017
19018
19019
19020
19021
19022
19023
19024
19025
19026
19027
19028
19029
19030
19031
19032
19033
19034
19035
19036
19037
19038
19039
19040
19041
19042
19043
19044
19045
19046
19047
19048
19049
19050
19051
19052
19053
19054
19055
19056
19057
19058
19059
19060
19061
19062
19063
19064
19065
19066
19067
19068
19069
19070
19071
19072
19073
19074
19075
19076
19077
19078
19079
19080
19081
19082
19083
19084
19085
19086
19087
19088
19089
19090
19091
19092
19093
19094
19095
19096
19097
19098
19099
19100
19101
19102
19103
19104
19105
19106
19107
19108
19109
19110
19111
19112
19113
19114
19115
19116
19117
19118
19119
19120
19121
19122
19123
19124
19125
19126
19127
19128
19129
19130
19131
19132
19133
19134
19135
19136
19137
19138
19139
19140
19141
19142
19143
19144
19145
19146
19147
19148
19149
19150
19151
19152
19153
19154
19155
19156
19157
19158
19159
19160
19161
19162
19163
19164
19165
19166
19167
19168
19169
19170
19171
19172
19173
19174
19175
19176
19177
19178
19179
19180
19181
19182
19183
19184
19185
19186
19187
19188
19189
19190
19191
19192
19193
19194
19195
19196
19197
19198
19199
19200
19201
19202
19203
19204
19205
19206
19207
19208
19209
19210
19211
19212
19213
19214
19215
19216
19217
19218
19219
19220
19221
19222
19223
19224
19225
19226
19227
19228
19229
19230
19231
19232
19233
19234
19235
19236
19237
19238
19239
19240
19241
19242
19243
19244
19245
19246
19247
19248
19249
19250
19251
19252
19253
19254
19255
19256
19257
19258
19259
19260
19261
19262
19263
19264
19265
19266
19267
19268
19269
19270
19271
19272
19273
19274
19275
19276
19277
19278
19279
19280
19281
19282
19283
19284
19285
19286
19287
19288
19289
19290
19291
19292
19293
19294
19295
19296
19297
19298
19299
19300
19301
19302
19303
19304
19305
19306
19307
19308
19309
19310
19311
19312
19313
19314
19315
19316
19317
19318
19319
19320
19321
19322
19323
19324
19325
19326
19327
19328
19329
19330
19331
19332
19333
19334
19335
19336
19337
19338
19339
19340
19341
19342
19343
19344
19345
19346
19347
19348
19349
19350
19351
19352
19353
19354
19355
19356
19357
19358
19359
19360
19361
19362
19363
19364
19365
19366
19367
19368
19369
19370
19371
19372
19373
19374
19375
19376
19377
19378
19379
19380
19381
19382
19383
19384
19385
19386
19387
19388
19389
19390
19391
19392
19393
19394
19395
19396
19397
19398
19399
19400
19401
19402
19403
19404
19405
19406
19407
19408
19409
19410
19411
19412
19413
19414
19415
19416
19417
19418
19419
19420
19421
19422
19423
19424
19425
19426
19427
19428
19429
19430
19431
19432
19433
19434
19435
19436
19437
19438
19439
19440
19441
19442
19443
19444
19445
19446
19447
19448
19449
19450
19451
19452
19453
19454
19455
19456
19457
19458
19459
19460
19461
19462
19463
19464
19465
19466
19467
19468
19469
19470
19471
19472
19473
19474
19475
19476
19477
19478
19479
19480
19481
19482
19483
19484
19485
19486
19487
19488
19489
19490
19491
19492
19493
19494
19495
19496
19497
19498
19499
19500
19501
19502
19503
19504
19505
19506
19507
19508
19509
19510
19511
19512
19513
19514
19515
19516
19517
19518
19519
19520
19521
19522
19523
19524
19525
19526
19527
19528
19529
19530
19531
19532
19533
19534
19535
19536
19537
19538
19539
19540
19541
19542
19543
19544
19545
19546
19547
19548
19549
19550
19551
19552
19553
19554
19555
19556
19557
19558
19559
19560
19561
19562
19563
19564
19565
19566
19567
19568
19569
19570
19571
19572
19573
19574
19575
19576
19577
19578
19579
19580
19581
19582
19583
19584
19585
19586
19587
19588
19589
19590
19591
19592
19593
19594
19595
19596
19597
19598
19599
19600
19601
19602
19603
19604
19605
19606
19607
19608
19609
19610
19611
19612
19613
19614
19615
19616
19617
19618
19619
19620
19621
19622
19623
19624
19625
19626
19627
19628
19629
19630
19631
19632
19633
19634
19635
19636
19637
19638
19639
19640
19641
19642
19643
19644
19645
19646
19647
19648
19649
19650
19651
19652
19653
19654
19655
19656
19657
19658
19659
19660
19661
19662
19663
19664
19665
19666
19667
19668
19669
19670
19671
19672
19673
19674
19675
19676
19677
19678
19679
19680
19681
19682
19683
19684
19685
19686
19687
19688
19689
19690
19691
19692
19693
19694
19695
19696
19697
19698
19699
19700
19701
19702
19703
19704
19705
19706
19707
19708
19709
19710
19711
19712
19713
19714
19715
19716
19717
19718
19719
19720
19721
19722
19723
19724
19725
19726
19727
19728
19729
19730
19731
19732
19733
19734
19735
19736
19737
19738
19739
19740
19741
19742
19743
19744
19745
19746
19747
19748
19749
19750
19751
19752
19753
19754
19755
19756
19757
19758
19759
19760
19761
19762
19763
19764
19765
19766
19767
19768
19769
19770
19771
19772
19773
19774
19775
19776
19777
19778
19779
19780
19781
19782
19783
19784
19785
19786
19787
19788
19789
19790
19791
19792
19793
19794
19795
19796
19797
19798
19799
19800
19801
19802
19803
19804
19805
19806
19807
19808
19809
19810
19811
19812
19813
19814
19815
19816
19817
19818
19819
19820
19821
19822
19823
19824
19825
19826
19827
19828
19829
19830
19831
19832
19833
19834
19835
19836
19837
19838
19839
19840
19841
19842
19843
19844
19845
19846
19847
19848
19849
19850
19851
19852
19853
19854
19855
19856
19857
19858
19859
19860
19861
19862
19863
19864
19865
19866
19867
19868
19869
19870
19871
19872
19873
19874
19875
19876
19877
19878
19879
19880
19881
19882
19883
19884
19885
19886
19887
19888
19889
19890
19891
19892
19893
19894
19895
19896
19897
19898
19899
19900
19901
19902
19903
19904
19905
19906
19907
19908
19909
19910
19911
19912
19913
19914
19915
19916
19917
19918
19919
19920
19921
19922
19923
19924
19925
19926
19927
19928
19929
19930
19931
19932
19933
19934
19935
19936
19937
19938
19939
19940
19941
19942
19943
19944
19945
19946
19947
19948
19949
19950
19951
19952
19953
19954
19955
19956
19957
19958
19959
19960
19961
19962
19963
19964
19965
19966
19967
19968
19969
19970
19971
19972
19973
19974
19975
19976
19977
19978
19979
19980
19981
19982
19983
19984
19985
19986
19987
19988
19989
19990
19991
19992
19993
19994
19995
19996
19997
19998
19999
20000
20001
20002
20003
20004
20005
20006
20007
20008
20009
20010
20011
20012
20013
20014
20015
20016
20017
20018
20019
20020
20021
20022
20023
20024
20025
20026
20027
20028
20029
20030
20031
20032
20033
20034
20035
20036
20037
20038
20039
20040
20041
20042
20043
20044
20045
20046
20047
20048
20049
20050
20051
20052
20053
20054
20055
20056
20057
20058
20059
20060
20061
20062
20063
20064
20065
20066
20067
20068
20069
20070
20071
20072
20073
20074
20075
20076
20077
20078
20079
20080
20081
20082
20083
20084
20085
20086
20087
20088
20089
20090
20091
20092
20093
20094
20095
20096
20097
20098
20099
20100
20101
20102
20103
20104
20105
20106
20107
20108
20109
20110
20111
20112
20113
20114
20115
20116
20117
20118
20119
20120
20121
20122
20123
20124
20125
20126
20127
20128
20129
20130
20131
20132
20133
20134
20135
20136
20137
20138
20139
20140
20141
20142
20143
20144
20145
20146
20147
20148
20149
20150
20151
20152
20153
20154
20155
20156
20157
20158
20159
20160
20161
20162
20163
20164
20165
20166
20167
20168
20169
20170
20171
20172
20173
20174
20175
20176
20177
20178
20179
20180
20181
20182
20183
20184
20185
20186
20187
20188
20189
20190
20191
20192
20193
20194
20195
20196
20197
20198
20199
20200
20201
20202
20203
20204
20205
20206
20207
20208
20209
20210
20211
20212
20213
20214
20215
20216
20217
20218
20219
20220
20221
20222
20223
20224
20225
20226
20227
20228
20229
20230
20231
20232
20233
20234
20235
20236
20237
20238
20239
20240
20241
20242
20243
20244
20245
20246
20247
20248
20249
20250
20251
20252
20253
20254
20255
20256
20257
20258
20259
20260
20261
20262
20263
20264
20265
20266
20267
20268
20269
20270
20271
20272
20273
20274
20275
20276
20277
20278
20279
20280
20281
20282
20283
20284
20285
20286
20287
20288
20289
20290
20291
20292
20293
20294
20295
20296
20297
20298
20299
20300
20301
20302
20303
20304
20305
20306
20307
20308
20309
20310
20311
20312
20313
20314
20315
20316
20317
20318
20319
20320
20321
20322
20323
20324
20325
20326
20327
20328
20329
20330
20331
20332
20333
20334
20335
20336
20337
20338
20339
20340
20341
20342
20343
20344
20345
20346
20347
20348
20349
20350
20351
20352
20353
20354
20355
20356
20357
20358
20359
20360
20361
20362
20363
20364
20365
20366
20367
20368
20369
20370
20371
20372
20373
20374
20375
20376
20377
20378
20379
20380
20381
20382
20383
20384
20385
20386
20387
20388
20389
20390
20391
20392
20393
20394
20395
20396
20397
20398
20399
20400
20401
20402
20403
20404
20405
20406
20407
20408
20409
20410
20411
20412
20413
20414
20415
20416
20417
20418
20419
20420
20421
20422
20423
20424
20425
20426
20427
20428
20429
20430
20431
20432
20433
20434
20435
20436
20437
20438
20439
20440
20441
20442
20443
20444
20445
20446
20447
20448
20449
20450
20451
20452
20453
20454
20455
20456
20457
20458
20459
20460
20461
20462
20463
20464
20465
20466
20467
20468
20469
20470
20471
20472
20473
20474
20475
20476
20477
20478
20479
20480
20481
20482
20483
20484
20485
20486
20487
20488
20489
20490
20491
20492
20493
20494
20495
20496
20497
20498
20499
20500
20501
20502
20503
20504
20505
20506
20507
20508
20509
20510
20511
20512
20513
20514
20515
20516
20517
20518
20519
20520
20521
20522
20523
20524
20525
20526
20527
20528
20529
20530
20531
20532
20533
20534
20535
20536
20537
20538
20539
20540
20541
20542
20543
20544
20545
20546
20547
20548
20549
20550
20551
20552
20553
20554
20555
20556
20557
20558
20559
20560
20561
20562
20563
20564
20565
20566
20567
20568
20569
20570
20571
20572
20573
20574
20575
20576
20577
20578
20579
20580
20581
20582
20583
20584
20585
20586
20587
20588
20589
20590
20591
20592
20593
20594
20595
20596
20597
20598
20599
20600
20601
20602
20603
20604
20605
20606
20607
20608
20609
20610
20611
20612
20613
20614
20615
20616
20617
20618
20619
20620
20621
20622
20623
20624
20625
20626
20627
20628
20629
20630
20631
20632
20633
20634
20635
20636
20637
20638
20639
20640
20641
20642
20643
20644
20645
20646
20647
20648
20649
20650
20651
20652
20653
20654
20655
20656
20657
20658
20659
20660
20661
20662
20663
20664
20665
20666
20667
20668
20669
20670
20671
20672
20673
20674
20675
20676
20677
20678
20679
20680
20681
20682
20683
20684
20685
20686
20687
20688
20689
20690
20691
20692
20693
20694
20695
20696
20697
20698
20699
20700
20701
20702
20703
20704
20705
20706
20707
20708
20709
20710
20711
20712
20713
20714
20715
20716
20717
20718
20719
20720
20721
20722
20723
20724
20725
20726
20727
20728
20729
20730
20731
20732
20733
20734
20735
20736
20737
20738
20739
20740
20741
20742
20743
20744
20745
20746
20747
20748
20749
20750
20751
20752
20753
20754
20755
20756
20757
20758
20759
20760
20761
20762
20763
20764
20765
20766
20767
20768
20769
20770
20771
20772
20773
20774
20775
20776
20777
20778
20779
20780
20781
20782
20783
20784
20785
20786
20787
20788
20789
20790
20791
20792
20793
20794
20795
20796
20797
20798
20799
20800
20801
20802
20803
20804
20805
20806
20807
20808
20809
20810
20811
20812
20813
20814
20815
20816
20817
20818
20819
20820
20821
20822
20823
20824
20825
20826
20827
20828
20829
20830
20831
20832
20833
20834
20835
20836
20837
20838
20839
20840
20841
20842
20843
20844
20845
20846
20847
20848
20849
20850
20851
20852
20853
20854
20855
20856
20857
20858
20859
20860
20861
20862
20863
20864
20865
20866
20867
20868
20869
20870
20871
20872
20873
20874
20875
20876
20877
20878
20879
20880
20881
20882
20883
20884
20885
20886
20887
20888
20889
20890
20891
20892
20893
20894
20895
20896
20897
20898
20899
20900
20901
20902
20903
20904
20905
20906
20907
20908
20909
20910
20911
20912
20913
20914
20915
20916
20917
20918
20919
20920
20921
20922
20923
20924
20925
20926
20927
20928
20929
20930
20931
20932
20933
20934
20935
20936
20937
20938
20939
20940
20941
20942
20943
20944
20945
20946
20947
20948
20949
20950
20951
20952
20953
20954
20955
20956
20957
20958
20959
20960
20961
20962
20963
20964
20965
20966
20967
20968
20969
20970
20971
20972
20973
20974
20975
20976
20977
20978
20979
20980
20981
20982
20983
20984
20985
20986
20987
20988
20989
20990
20991
20992
20993
20994
20995
20996
20997
20998
20999
21000
21001
21002
21003
21004
21005
21006
21007
21008
21009
21010
21011
21012
21013
21014
21015
21016
21017
21018
21019
21020
21021
21022
21023
21024
21025
21026
21027
21028
21029
21030
21031
21032
21033
21034
21035
21036
21037
21038
21039
21040
21041
21042
21043
21044
21045
21046
21047
21048
21049
21050
21051
21052
21053
21054
21055
21056
21057
21058
21059
21060
21061
21062
21063
21064
21065
21066
21067
21068
21069
21070
21071
21072
21073
21074
21075
21076
21077
21078
21079
21080
21081
21082
21083
21084
21085
21086
21087
21088
21089
21090
21091
21092
21093
21094
21095
21096
21097
21098
21099
21100
21101
21102
21103
21104
21105
21106
21107
21108
21109
21110
21111
21112
21113
21114
21115
21116
21117
21118
21119
21120
21121
21122
21123
21124
21125
21126
21127
21128
21129
21130
21131
21132
21133
21134
21135
21136
21137
21138
21139
21140
21141
21142
21143
21144
21145
21146
21147
21148
21149
21150
21151
21152
21153
21154
21155
21156
21157
21158
21159
21160
21161
21162
21163
21164
21165
21166
21167
21168
21169
21170
21171
21172
21173
21174
21175
21176
21177
21178
21179
21180
21181
21182
21183
21184
21185
21186
21187
21188
21189
21190
21191
21192
21193
21194
21195
21196
21197
21198
21199
21200
21201
21202
21203
21204
21205
21206
21207
21208
21209
21210
21211
21212
21213
21214
21215
21216
21217
21218
21219
21220
21221
21222
21223
21224
21225
21226
21227
21228
21229
21230
21231
21232
21233
21234
21235
21236
21237
21238
21239
21240
21241
21242
21243
21244
21245
21246
21247
21248
21249
21250
21251
21252
21253
21254
21255
21256
21257
21258
21259
21260
21261
21262
21263
21264
21265
21266
21267
21268
21269
21270
21271
21272
21273
21274
21275
21276
21277
21278
21279
21280
21281
21282
21283
21284
21285
21286
21287
21288
21289
21290
21291
21292
21293
21294
21295
21296
21297
21298
21299
21300
21301
21302
21303
21304
21305
21306
21307
21308
21309
21310
21311
21312
21313
21314
21315
21316
21317
21318
21319
21320
21321
21322
21323
21324
21325
21326
21327
21328
21329
21330
21331
21332
21333
21334
21335
21336
21337
21338
21339
21340
21341
21342
21343
21344
21345
21346
21347
21348
21349
21350
21351
21352
21353
21354
21355
21356
21357
21358
21359
21360
21361
21362
21363
21364
21365
21366
21367
21368
21369
21370
21371
21372
21373
21374
21375
21376
21377
21378
21379
21380
21381
21382
21383
21384
21385
21386
21387
21388
21389
21390
21391
21392
21393
21394
21395
21396
21397
21398
21399
21400
21401
21402
21403
21404
21405
21406
21407
21408
21409
21410
21411
21412
21413
21414
21415
21416
21417
21418
21419
21420
21421
21422
21423
21424
21425
21426
21427
21428
21429
21430
21431
21432
21433
21434
21435
21436
21437
21438
21439
21440
21441
21442
21443
21444
21445
21446
21447
21448
21449
21450
21451
21452
21453
21454
21455
21456
21457
21458
21459
21460
21461
21462
21463
21464
21465
21466
21467
21468
21469
21470
21471
21472
21473
21474
21475
21476
21477
21478
21479
21480
21481
21482
21483
21484
21485
21486
21487
21488
21489
21490
21491
21492
21493
21494
21495
21496
21497
21498
21499
21500
21501
21502
21503
21504
21505
21506
21507
21508
21509
21510
21511
21512
21513
21514
21515
21516
21517
21518
21519
21520
21521
21522
21523
21524
21525
21526
21527
21528
21529
21530
21531
21532
21533
21534
21535
21536
21537
21538
21539
21540
21541
21542
21543
21544
21545
21546
21547
21548
21549
21550
21551
21552
21553
21554
21555
21556
21557
21558
21559
21560
21561
21562
21563
21564
21565
21566
21567
21568
21569
21570
21571
21572
21573
21574
21575
21576
21577
21578
21579
21580
21581
21582
21583
21584
21585
21586
21587
21588
21589
21590
21591
21592
21593
21594
21595
21596
21597
21598
21599
21600
21601
21602
21603
21604
21605
21606
21607
21608
21609
21610
21611
21612
21613
21614
21615
21616
21617
21618
21619
21620
21621
21622
21623
21624
21625
21626
21627
21628
21629
21630
21631
21632
21633
21634
21635
21636
21637
21638
21639
21640
21641
21642
21643
21644
21645
21646
21647
21648
21649
21650
21651
21652
21653
21654
21655
21656
21657
21658
21659
21660
21661
21662
21663
21664
21665
21666
21667
21668
21669
21670
21671
21672
21673
21674
21675
21676
21677
21678
21679
21680
21681
21682
21683
21684
21685
21686
21687
21688
21689
21690
21691
21692
21693
21694
21695
21696
21697
21698
21699
21700
21701
21702
21703
21704
21705
21706
21707
21708
21709
21710
21711
21712
21713
21714
21715
21716
21717
21718
21719
21720
21721
21722
21723
21724
21725
21726
21727
21728
21729
21730
21731
21732
21733
21734
21735
21736
21737
21738
21739
21740
21741
21742
21743
21744
21745
21746
21747
21748
21749
21750
21751
21752
21753
21754
21755
21756
21757
21758
21759
21760
21761
21762
21763
21764
21765
21766
21767
21768
21769
21770
21771
21772
21773
21774
21775
21776
21777
21778
21779
21780
21781
21782
21783
21784
21785
21786
21787
21788
21789
21790
21791
21792
21793
21794
21795
21796
21797
21798
21799
21800
21801
21802
21803
21804
21805
21806
21807
21808
21809
21810
21811
21812
21813
21814
21815
21816
21817
21818
21819
21820
21821
21822
21823
21824
21825
21826
21827
21828
21829
21830
21831
21832
21833
21834
21835
21836
21837
21838
21839
21840
21841
21842
21843
21844
21845
21846
21847
21848
21849
21850
21851
21852
21853
21854
21855
21856
21857
21858
21859
21860
21861
21862
21863
21864
21865
21866
21867
21868
21869
21870
21871
21872
21873
21874
21875
21876
21877
21878
21879
21880
21881
21882
21883
21884
21885
21886
21887
21888
21889
21890
21891
21892
21893
21894
21895
21896
21897
21898
21899
21900
21901
21902
21903
21904
21905
21906
21907
21908
21909
21910
21911
21912
21913
21914
21915
21916
21917
21918
21919
21920
21921
21922
21923
21924
21925
21926
21927
21928
21929
21930
21931
21932
21933
21934
21935
21936
21937
21938
21939
21940
21941
21942
21943
21944
21945
21946
21947
21948
21949
21950
21951
21952
21953
21954
21955
21956
21957
21958
21959
21960
21961
21962
21963
21964
21965
21966
21967
21968
21969
21970
21971
21972
21973
21974
21975
21976
21977
21978
21979
21980
21981
21982
21983
21984
21985
21986
21987
21988
21989
21990
21991
21992
21993
21994
21995
21996
21997
21998
21999
22000
22001
22002
22003
22004
22005
22006
22007
22008
22009
22010
22011
22012
22013
22014
22015
22016
22017
22018
22019
22020
22021
22022
22023
22024
22025
22026
22027
22028
22029
22030
22031
22032
22033
22034
22035
22036
22037
22038
22039
22040
22041
22042
22043
22044
22045
22046
22047
22048
22049
22050
22051
22052
22053
22054
22055
22056
22057
22058
22059
22060
22061
22062
22063
22064
22065
22066
22067
22068
22069
22070
22071
22072
22073
22074
22075
22076
22077
22078
22079
22080
22081
22082
22083
22084
22085
22086
22087
22088
22089
22090
22091
22092
22093
22094
22095
22096
22097
22098
22099
22100
22101
22102
22103
22104
22105
22106
22107
22108
22109
22110
22111
22112
22113
22114
22115
22116
22117
22118
22119
22120
22121
22122
22123
22124
22125
22126
22127
22128
22129
22130
22131
22132
22133
22134
22135
22136
22137
22138
22139
22140
22141
22142
22143
22144
22145
22146
22147
22148
22149
22150
22151
22152
22153
22154
22155
22156
22157
22158
22159
22160
22161
22162
22163
22164
22165
22166
22167
22168
22169
22170
22171
22172
22173
22174
22175
22176
22177
22178
22179
22180
22181
22182
22183
22184
22185
22186
22187
22188
22189
22190
22191
22192
22193
22194
22195
22196
22197
22198
22199
22200
22201
22202
22203
22204
22205
22206
22207
22208
22209
22210
22211
22212
22213
22214
22215
22216
22217
22218
22219
22220
22221
22222
22223
22224
22225
22226
22227
22228
22229
22230
22231
22232
22233
22234
22235
22236
22237
22238
22239
22240
22241
22242
22243
22244
22245
22246
22247
22248
22249
22250
22251
22252
22253
22254
22255
22256
22257
22258
22259
22260
22261
22262
22263
22264
22265
22266
22267
22268
22269
22270
22271
22272
22273
22274
22275
22276
22277
22278
22279
22280
22281
22282
22283
22284
22285
22286
22287
22288
22289
22290
22291
22292
22293
22294
22295
22296
22297
22298
22299
22300
22301
22302
22303
22304
22305
22306
22307
22308
22309
22310
22311
22312
22313
22314
22315
22316
22317
22318
22319
22320
22321
22322
22323
22324
22325
22326
22327
22328
22329
22330
22331
22332
22333
22334
22335
22336
22337
22338
22339
22340
22341
22342
22343
22344
22345
22346
22347
22348
22349
22350
22351
22352
22353
22354
22355
22356
22357
22358
22359
22360
22361
22362
22363
22364
22365
22366
22367
22368
22369
22370
22371
22372
22373
22374
22375
22376
22377
22378
22379
22380
22381
22382
22383
22384
22385
22386
22387
22388
22389
22390
22391
22392
22393
22394
22395
22396
22397
22398
22399
22400
22401
22402
22403
22404
22405
22406
22407
22408
22409
22410
22411
22412
22413
22414
22415
22416
22417
22418
22419
22420
22421
22422
22423
22424
22425
22426
22427
22428
22429
22430
22431
22432
22433
22434
22435
22436
22437
22438
22439
22440
22441
22442
22443
22444
22445
22446
22447
22448
22449
22450
22451
22452
22453
22454
22455
22456
22457
22458
22459
22460
22461
22462
22463
22464
22465
22466
22467
22468
22469
22470
22471
22472
22473
22474
22475
22476
22477
22478
22479
22480
22481
22482
22483
22484
22485
22486
22487
22488
22489
22490
22491
22492
22493
22494
22495
22496
22497
22498
22499
22500
22501
22502
22503
22504
22505
22506
22507
22508
22509
22510
22511
22512
22513
22514
22515
22516
22517
22518
22519
22520
22521
22522
22523
22524
22525
22526
22527
22528
22529
22530
22531
22532
22533
22534
22535
22536
22537
22538
22539
22540
22541
22542
22543
22544
22545
22546
22547
22548
22549
22550
22551
22552
22553
22554
22555
22556
22557
22558
22559
22560
22561
22562
22563
22564
22565
22566
22567
22568
22569
22570
22571
22572
22573
22574
22575
22576
22577
22578
22579
22580
22581
22582
22583
22584
22585
22586
22587
22588
22589
22590
22591
22592
22593
22594
22595
22596
22597
22598
22599
22600
22601
22602
22603
22604
22605
22606
22607
22608
22609
22610
22611
22612
22613
22614
22615
22616
22617
22618
22619
22620
22621
22622
22623
22624
22625
22626
22627
22628
22629
22630
22631
22632
22633
22634
22635
22636
22637
22638
22639
22640
22641
22642
22643
22644
22645
22646
22647
22648
22649
22650
22651
22652
22653
22654
22655
22656
22657
22658
22659
22660
22661
22662
22663
22664
22665
22666
22667
22668
22669
22670
22671
22672
22673
22674
22675
22676
22677
22678
22679
22680
22681
22682
22683
22684
22685
22686
22687
22688
22689
22690
22691
22692
22693
22694
22695
22696
22697
22698
22699
22700
22701
22702
22703
22704
22705
22706
22707
22708
22709
22710
22711
22712
22713
22714
22715
22716
22717
22718
22719
22720
22721
22722
22723
22724
22725
22726
22727
22728
22729
22730
22731
22732
22733
22734
22735
22736
22737
22738
22739
22740
22741
22742
22743
22744
22745
22746
22747
22748
22749
22750
22751
22752
22753
22754
22755
22756
22757
22758
22759
22760
22761
22762
22763
22764
22765
22766
22767
22768
22769
22770
22771
22772
22773
22774
22775
22776
22777
22778
22779
22780
22781
22782
22783
22784
22785
22786
22787
22788
22789
22790
22791
22792
22793
22794
22795
22796
22797
22798
22799
22800
22801
22802
22803
22804
22805
22806
22807
22808
22809
22810
22811
22812
22813
22814
22815
22816
22817
22818
22819
22820
22821
22822
22823
22824
22825
22826
22827
22828
22829
22830
22831
22832
22833
22834
22835
22836
22837
22838
22839
22840
22841
22842
22843
22844
22845
22846
22847
22848
22849
22850
22851
22852
22853
22854
22855
22856
22857
22858
22859
22860
22861
22862
22863
22864
22865
22866
22867
22868
22869
22870
22871
22872
22873
22874
22875
22876
22877
22878
22879
22880
22881
22882
22883
22884
22885
22886
22887
22888
22889
22890
22891
22892
22893
22894
22895
22896
22897
22898
22899
22900
22901
22902
22903
22904
22905
22906
22907
22908
22909
22910
22911
22912
22913
22914
22915
22916
22917
22918
22919
22920
22921
22922
22923
22924
22925
22926
22927
22928
22929
22930
22931
22932
22933
22934
22935
22936
22937
22938
22939
22940
22941
22942
22943
22944
22945
22946
22947
22948
22949
22950
22951
22952
22953
22954
22955
22956
22957
22958
22959
22960
22961
22962
22963
22964
22965
22966
22967
22968
22969
22970
22971
22972
22973
22974
22975
22976
22977
22978
22979
22980
22981
22982
22983
22984
22985
22986
22987
22988
22989
22990
22991
22992
22993
22994
22995
22996
22997
22998
22999
23000
23001
23002
23003
23004
23005
23006
23007
23008
23009
23010
23011
23012
23013
23014
23015
23016
23017
23018
23019
23020
23021
23022
23023
23024
23025
23026
23027
23028
23029
23030
23031
23032
23033
23034
23035
23036
23037
23038
23039
23040
23041
23042
23043
23044
23045
23046
23047
23048
23049
23050
23051
23052
23053
23054
23055
23056
23057
23058
23059
23060
23061
23062
23063
23064
23065
23066
23067
23068
23069
23070
23071
23072
23073
23074
23075
23076
23077
23078
23079
23080
23081
23082
23083
23084
23085
23086
23087
23088
23089
23090
23091
23092
23093
23094
23095
23096
23097
23098
23099
23100
23101
23102
23103
23104
23105
23106
23107
23108
23109
23110
23111
23112
23113
23114
23115
23116
23117
23118
23119
23120
23121
23122
23123
23124
23125
23126
23127
23128
23129
23130
23131
23132
23133
23134
23135
23136
23137
23138
23139
23140
23141
23142
23143
23144
23145
23146
23147
23148
23149
23150
23151
23152
23153
23154
23155
23156
23157
23158
23159
23160
23161
23162
23163
23164
23165
23166
23167
23168
23169
23170
23171
23172
23173
23174
23175
23176
23177
23178
23179
23180
23181
23182
23183
23184
23185
23186
23187
23188
23189
23190
23191
23192
23193
23194
23195
23196
23197
23198
23199
23200
23201
23202
23203
23204
23205
23206
23207
23208
23209
23210
23211
23212
23213
23214
23215
23216
23217
23218
23219
23220
23221
23222
23223
23224
23225
23226
23227
23228
23229
23230
23231
23232
23233
23234
23235
23236
23237
23238
23239
23240
23241
23242
23243
23244
23245
23246
23247
23248
23249
23250
23251
23252
23253
23254
23255
23256
23257
23258
23259
23260
23261
23262
23263
23264
23265
23266
23267
23268
23269
23270
23271
23272
23273
23274
23275
23276
23277
23278
23279
23280
23281
23282
23283
23284
23285
23286
23287
23288
23289
23290
23291
23292
23293
23294
23295
23296
23297
23298
23299
23300
23301
23302
23303
23304
23305
23306
23307
23308
23309
23310
23311
23312
23313
23314
23315
23316
23317
23318
23319
23320
23321
23322
23323
23324
23325
23326
23327
23328
23329
23330
23331
23332
23333
23334
23335
23336
23337
23338
23339
23340
23341
23342
23343
23344
23345
23346
23347
23348
23349
23350
23351
23352
23353
23354
23355
23356
23357
23358
23359
23360
23361
23362
23363
23364
23365
23366
23367
23368
23369
23370
23371
23372
23373
23374
23375
23376
23377
23378
23379
23380
23381
23382
23383
23384
23385
23386
23387
23388
23389
23390
23391
23392
23393
23394
23395
23396
23397
23398
23399
23400
23401
23402
23403
23404
23405
23406
23407
23408
23409
23410
23411
23412
23413
23414
23415
23416
23417
23418
23419
23420
23421
23422
23423
23424
23425
23426
23427
23428
23429
23430
23431
23432
23433
23434
23435
23436
23437
23438
23439
23440
23441
23442
23443
23444
23445
23446
23447
23448
23449
23450
23451
23452
23453
23454
23455
23456
23457
23458
23459
23460
23461
23462
23463
23464
23465
23466
23467
23468
23469
23470
23471
23472
23473
23474
23475
23476
23477
23478
23479
23480
23481
23482
23483
23484
23485
23486
23487
23488
23489
23490
23491
23492
23493
23494
23495
23496
23497
23498
23499
23500
23501
23502
23503
23504
23505
23506
23507
23508
23509
23510
23511
23512
23513
23514
23515
23516
23517
23518
23519
23520
23521
23522
23523
23524
23525
23526
23527
23528
23529
23530
23531
23532
23533
23534
23535
23536
23537
23538
23539
23540
23541
23542
23543
23544
23545
23546
23547
23548
23549
23550
23551
23552
23553
23554
23555
23556
23557
23558
23559
23560
23561
23562
23563
23564
23565
23566
23567
23568
23569
23570
23571
23572
23573
23574
23575
23576
23577
23578
23579
23580
23581
23582
23583
23584
23585
23586
23587
23588
23589
23590
23591
23592
23593
23594
23595
23596
23597
23598
23599
23600
23601
23602
23603
23604
23605
23606
23607
23608
23609
23610
23611
23612
23613
23614
23615
23616
23617
23618
23619
23620
23621
23622
23623
23624
23625
23626
23627
23628
23629
23630
23631
23632
23633
23634
23635
23636
23637
23638
23639
23640
23641
23642
23643
23644
23645
23646
23647
23648
23649
23650
23651
23652
23653
23654
23655
23656
23657
23658
23659
23660
23661
23662
23663
23664
23665
23666
23667
23668
23669
23670
23671
23672
23673
23674
23675
23676
23677
23678
23679
23680
23681
23682
23683
23684
23685
23686
23687
23688
23689
23690
23691
23692
23693
23694
23695
23696
23697
23698
23699
23700
23701
23702
23703
23704
23705
23706
23707
23708
23709
23710
23711
23712
23713
23714
23715
23716
23717
23718
23719
23720
23721
23722
23723
23724
23725
23726
23727
23728
23729
23730
23731
23732
23733
23734
23735
23736
23737
23738
23739
23740
23741
23742
23743
23744
23745
23746
23747
23748
23749
23750
23751
23752
23753
23754
23755
23756
23757
23758
23759
23760
23761
23762
23763
23764
23765
23766
23767
23768
23769
23770
23771
23772
23773
23774
23775
23776
23777
23778
23779
23780
23781
23782
23783
23784
23785
23786
23787
23788
23789
23790
23791
23792
23793
23794
23795
23796
23797
23798
23799
23800
23801
23802
23803
23804
23805
23806
23807
23808
23809
23810
23811
23812
23813
23814
23815
23816
23817
23818
23819
23820
23821
23822
23823
23824
23825
23826
23827
23828
23829
23830
23831
23832
23833
23834
23835
23836
23837
23838
23839
23840
23841
23842
23843
23844
23845
23846
23847
23848
23849
23850
23851
23852
23853
23854
23855
23856
23857
23858
23859
23860
23861
23862
23863
23864
23865
23866
23867
23868
23869
23870
23871
23872
23873
23874
23875
23876
23877
23878
23879
23880
23881
23882
23883
23884
23885
23886
23887
23888
23889
23890
23891
23892
23893
23894
23895
23896
23897
23898
23899
23900
23901
23902
23903
23904
23905
23906
23907
23908
23909
23910
23911
23912
23913
23914
23915
23916
23917
23918
23919
23920
23921
23922
23923
23924
23925
23926
23927
23928
23929
23930
23931
23932
23933
23934
23935
23936
23937
23938
23939
23940
23941
23942
23943
23944
23945
23946
23947
23948
23949
23950
23951
23952
23953
23954
23955
23956
23957
23958
23959
23960
23961
23962
23963
23964
23965
23966
23967
23968
23969
23970
23971
23972
23973
23974
23975
23976
23977
23978
23979
23980
23981
23982
23983
23984
23985
23986
23987
23988
23989
23990
23991
23992
23993
23994
23995
23996
23997
23998
23999
24000
24001
24002
24003
24004
24005
24006
24007
24008
24009
24010
24011
24012
24013
24014
24015
24016
24017
24018
24019
24020
24021
24022
24023
24024
24025
24026
24027
24028
24029
24030
24031
24032
24033
24034
24035
24036
24037
24038
24039
24040
24041
24042
24043
24044
24045
24046
24047
24048
24049
24050
24051
24052
24053
24054
24055
24056
24057
24058
24059
24060
24061
24062
24063
24064
24065
24066
24067
24068
24069
24070
24071
24072
24073
24074
24075
24076
24077
24078
24079
24080
24081
24082
24083
24084
24085
24086
24087
24088
24089
24090
24091
24092
24093
24094
24095
24096
24097
24098
24099
24100
24101
24102
24103
24104
24105
24106
24107
24108
24109
24110
24111
24112
24113
24114
24115
24116
24117
24118
24119
24120
24121
24122

 
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014-2024 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016-2024 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018-2024 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019, 2020, 2021, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com>
;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2022, 2023, 2024 Navid Afkhami <navid.afkhami@mdc-berlin.de>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2024 Alexis Simon <alexis.simon@runbox.com>
;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages bioinformatics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix gexp)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix hg-download)
  #:use-module (guix build-system ant)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cargo)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system go)
  #:use-module (guix build-system haskell)
  #:use-module (guix build-system meson)
  #:use-module (guix build-system perl)
  #:use-module (guix build-system pyproject)
  #:use-module (guix build-system python)
  #:use-module (guix build-system qt)
  #:use-module (guix build-system r)
  #:use-module (guix build-system ruby)
  #:use-module (guix build-system trivial)
  #:use-module (guix deprecation)
  #:use-module (gnu packages)
  #:use-module (gnu packages admin)
  #:use-module (gnu packages assembly)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages bioconductor)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages code)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages cpio)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages crates-io)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages docbook)
  #:use-module (gnu packages documentation)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages datastructures)
  #:use-module (gnu packages dlang)
  #:use-module (gnu packages file)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages gawk)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gd)
  #:use-module (gnu packages golang)
  #:use-module (gnu packages golang-build)
  #:use-module (gnu packages golang-check)
  #:use-module (gnu packages golang-compression)
  #:use-module (gnu packages golang-xyz)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages groff)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages guile)
  #:use-module (gnu packages guile-xyz)
  #:use-module (gnu packages haskell-check)
  #:use-module (gnu packages haskell-web)
  #:use-module (gnu packages haskell-xyz)
  #:use-module (gnu packages image)
  #:use-module (gnu packages image-processing)
  #:use-module (gnu packages imagemagick)
  #:use-module (gnu packages java)
  #:use-module (gnu packages java-compression)
  #:use-module (gnu packages java-xml)
  #:use-module (gnu packages jemalloc)
  #:use-module (gnu packages jupyter)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages logging)
  #:use-module (gnu packages lsof)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages man)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages node)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages parallel)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages perl-check)
  #:use-module (gnu packages perl-web)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages popt)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-compression)
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages rdf)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages rpc)
  #:use-module (gnu packages rsync)
  #:use-module (gnu packages ruby)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages shells)
  #:use-module (gnu packages skribilo)
  #:use-module (gnu packages sphinx)
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages swig)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages tex)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages time)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages uglifyjs)
  #:use-module (gnu packages video)
  #:use-module (gnu packages vim)
  #:use-module (gnu packages web)
  #:use-module (gnu packages wget)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (guix platform)
  #:use-module (srfi srfi-1)
  #:use-module (srfi srfi-26)
  #:use-module (ice-9 match))

(define-public aragorn
  (package
    (name "aragorn")
    (version "1.2.41")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.ansikte.se/ARAGORN/Downloads/"
                                  "aragorn" version ".c"))
              (sha256
               (base32
                "0jkzx7sqiarydvz3bwaxh790fpvpkfc926dhsza1dbdhq32ir8wj"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f ; there are no tests
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (replace 'build
            (lambda _
              (invoke "gcc" "-O3" "-ffast-math" "-finline-functions"
                      "-o" "aragorn" #$source)))
          (replace 'install
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((bin (string-append #$output "/bin"))
                    (man (string-append #$output "/share/man/man1")))
                (install-file "aragorn" bin)
                (mkdir-p man)
                (copy-file (assoc-ref inputs "aragorn.1")
                           (string-append man "/aragorn.1"))))))))
    (native-inputs
     `(("aragorn.1"
        ,(origin
           (method url-fetch)
           (uri "https://www.ansikte.se/ARAGORN/Downloads/aragorn.1")
           (sha256
            (base32
             "0bn9lapa6f0cl07dbn2fjrapirv9d4bk7w248w39fhb4vbczcc3f"))))))
    (home-page "https://www.ansikte.se/ARAGORN/")
    (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
    (description
     "Aragorn identifies transfer RNA, mitochondrial RNA and
transfer-messenger RNA from nucleotide sequences, based on homology to known
tRNA consensus sequences and RNA structure.  It also outputs the secondary
structure of the predicted RNA.")
    (license license:gpl3+)))

(define-public bamtools
  (package
    (name "bamtools")
    (version "2.5.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/pezmaster31/bamtools")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "14lw571vbks138i0lj66qjdbk8iwa817x2zbpzij61vv1gdgfbn5"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      '(list "-DBUILD_SHARED_LIBS=ON")))
    (inputs (list jsoncpp zlib))
    (native-inputs (list pkg-config))
    (home-page "https://github.com/pezmaster31/bamtools")
    (synopsis "C++ API and command-line toolkit for working with BAM data")
    (description
     "BamTools provides both a C++ API and a command-line toolkit for handling
BAM files.")
    (license license:expat)))

(define-public bamutils
  (package
    (name "bamutils")
    (version "1.0.15")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/statgen/bamUtil")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1pxydf9qsr8667jh525bc2wiqn9nwk8rkg05kbyfmjs8d261fl9y"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f ;fails to link debug libraries
      #:test-target "test"
      #:make-flags
      #~(list (string-append "INSTALLDIR=" #$output "/bin"))
      #:phases
      #~(modify-phases %standard-phases
          (replace 'configure
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "src/Makefile"
                (("^DATE=.*") "DATE=\"1970-01-01\"\n"))
              (copy-recursively (assoc-ref inputs "libstatgen")
                                "../libStatGen"))))))
    (inputs
     (list zlib))
    (native-inputs
     `(("libstatgen"
        ,(origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/statgen/libStatGen/")
                 (commit (string-append "v" version))))
           (file-name (git-file-name "libstatgen" version))
           (sha256
            (base32
             "0spvbpvnpxrgj8kajpkhf1mv7kdyvj723y9zh13jykvnjh8a15j3"))))))
    (home-page "https://genome.sph.umich.edu/wiki/BamUtil")
    (synopsis "Programs for working on SAM/BAM files")
    (description "This package provides several programs that perform
operations on SAM/BAM files.  All of these programs are built into a
single executable called @code{bam}.")
    (license license:gpl3+)))

(define-public bcftools
  (package
    (name "bcftools")
    (version "1.14")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/samtools/bcftools/"
                                  "releases/download/"
                                  version "/bcftools-" version ".tar.bz2"))
              (sha256
               (base32
                "1jqrma16fx8kpvb3c0462dg0asvmiv5yi8myqmc5ddgwi6p8ivxp"))
              (modules '((guix build utils)))
              (snippet '(begin
                          ;; Delete bundled htslib.
                          (delete-file-recursively "htslib-1.14")))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       (list "--enable-libgsl")
       #:test-target "test"
       #:phases
       (modify-phases %standard-phases
         (add-before 'check 'patch-tests
           (lambda _
             (substitute* "test/test.pl"
               (("/bin/bash") (which "bash"))))))))
    (native-inputs
     (list htslib perl))
    (inputs
     (list gsl zlib))
    (home-page "https://samtools.github.io/bcftools/")
    (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
    (description
     "BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF.  All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
    ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
    (license (list license:gpl3+ license:expat))))

(define-public bcftools-1.12
  (package/inherit bcftools
    (version "1.12")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/samtools/bcftools/"
                                  "releases/download/"
                                  version "/bcftools-" version ".tar.bz2"))
              (sha256
               (base32
                "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
              (modules '((guix build utils)))
              (snippet '(begin
                          ;; Delete bundled htslib.
                          (delete-file-recursively "htslib-1.12")))))
    (native-inputs (list htslib-1.12 perl))))

(define-public bcftools-1.10
  (package/inherit bcftools
    (version "1.10")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/samtools/bcftools/"
                                  "releases/download/"
                                  version "/bcftools-" version ".tar.bz2"))
              (sha256
               (base32
                "10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra"))
              (modules '((guix build utils)))
              (snippet '(begin
                          ;; Delete bundled htslib.
                          (delete-file-recursively "htslib-1.10")))))
    (native-inputs (list htslib-1.10 perl))))

(define-public bedops
  (package
    (name "bedops")
    (version "2.4.41")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/bedops/bedops")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l"))))
    (build-system gnu-build-system)
    (arguments
     (list
      ;; We cannot run the tests because the build system makes strange
      ;; assumptions about where executables are located.
      #:tests? #false
      #:test-target "tests"
      #:make-flags
      #~(list (string-append "CC=" #$(cc-for-target)))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'unpack-tarballs
            (lambda _
              ;; FIXME: Bedops includes tarballs of minimally patched upstream
              ;; libraries jansson, zlib, and bzip2.  We cannot just use stock
              ;; libraries because at least one of the libraries (zlib) is
              ;; patched to add a C++ function definition (deflateInit2cpp).
              ;; Until the Bedops developers offer a way to link against system
              ;; libraries we have to build the in-tree copies of these three
              ;; libraries.

              ;; See upstream discussion:
              ;; https://github.com/bedops/bedops/issues/124

              ;; Unpack the tarballs to benefit from shebang patching.
              (with-directory-excursion "third-party"
                (invoke "tar" "xvf" "jansson-2.6.tar.bz2")
                (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
                (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2"))
              ;; Disable unpacking of tarballs in Makefile.
              (substitute* "system.mk/Makefile.linux"
                (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
                (("\\./configure") "CONFIG_SHELL=bash ./configure"))
              (substitute* "third-party/zlib-1.2.7/Makefile.in"
                (("^SHELL=.*$") "SHELL=bash\n"))))
          (delete 'configure)
          (replace 'install
            (lambda _
              (invoke "make" "install"
                      (string-append "BINDIR=" #$output "/bin")))))))
    (native-inputs
     (list diffutils perl which))
    (home-page "https://github.com/bedops/bedops")
    (synopsis "Tools for high-performance genomic feature operations")
    (description
     "BEDOPS is a suite of tools to address common questions raised in genomic
studies---mostly with regard to overlap and proximity relationships between
data sets.  It aims to be scalable and flexible, facilitating the efficient
and accurate analysis and management of large-scale genomic data.

BEDOPS provides tools that perform highly efficient and scalable Boolean and
other set operations, statistical calculations, archiving, conversion and
other management of genomic data of arbitrary scale.  Tasks can be easily
split by chromosome for distributing whole-genome analyses across a
computational cluster.")
    (license license:gpl2+)))

(define-public bedtools
  (package
    (name "bedtools")
    (version "2.30.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
                                  "download/v" version "/"
                                  "bedtools-" version ".tar.gz"))
              (sha256
               (base32
                "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:test-target "test"
      #:make-flags
      #~(list (string-append "prefix=" #$output))
      #:phases
      '(modify-phases %standard-phases
         (delete 'configure))))
    (native-inputs
     (list python-wrapper))
    (inputs
     (list samtools zlib))
    (home-page "https://github.com/arq5x/bedtools2")
    (synopsis "Tools for genome analysis and arithmetic")
    (description
     "Collectively, the bedtools utilities are a swiss-army knife of tools for
a wide-range of genomics analysis tasks.  The most widely-used tools enable
genome arithmetic: that is, set theory on the genome.  For example, bedtools
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
    (license license:expat)))

;; Later releases of bedtools produce files with more columns than
;; what Ribotaper expects.
(define-public bedtools-2.18
  (package (inherit bedtools)
    (name "bedtools")
    (version "2.18.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/arq5x/bedtools2/"
                                  "releases/download/v" version
                                  "/bedtools-" version ".tar.gz"))
              (sha256
               (base32
                "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz"))))
    (arguments
     (list
      #:test-target "test"
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'compatibility
            (lambda _
              (substitute* "src/utils/fileType/FileRecordTypeChecker.h"
                (("static const float PERCENTAGE")
                 "static constexpr float PERCENTAGE"))
              (substitute* "src/utils/general/DualQueue.h"
                (("template <class T, template<class T> class CompareFunc>")
                 "template <class T, template<class U> class CompareFunc>"))
              (substitute* '("src/utils/BamTools/src/api/algorithms/Sort.h"
                             "src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h")
                (("(bool operator\\(\\).*) \\{" m pre)
                 (string-append pre " const {")))))
          (delete 'configure)
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin/")))
                (for-each (lambda (file)
                            (install-file file bin))
                          (find-files "bin" ".*"))))))))
    (native-inputs
     (list python-wrapper))
    (inputs
     (list samtools zlib))))

(define-public bitmapperbs
  (package
    (name "bitmapperbs")
    (version "1.0.2.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/chhylp123/BitMapperBS/")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "02ksssfnvmpskld0a2016smfz5nrzm3d90v8974f3cpzywckvp8v"))
              (modules '((guix build utils)))
              ;; This package bundles a modified copy of htslib, so we cannot
              ;; unbundle it.
              (snippet
               '(begin
                  (delete-file-recursively "libdivsufsort-2.0.1")
                  (delete-file-recursively "pSAscan-0.1.0")))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #false
      #:make-flags '(list "bitmapperBS")
      ;; The build system checks for CPU features.  For this reason, we want
      ;; users to build it locally instead of using substitutes.
      #:substitutable? #false
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-build-system
            (lambda _
              (substitute* "Makefile"
                (("make prefix=../htslib_aim install")
                 (string-append "make prefix=" #$output " install-so"))
                (("htslib_aim/include") "htslib")
                (("htslib_aim/lib")
                 (string-append #$output "/lib")))))
          (add-after 'unpack 'patch-references-to-psascan
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "Makefile"
                (("\"(./)?psascan" pre all)
                 (string-append "\"" pre (search-input-file inputs "/bin/psascan"))))))
          (delete 'configure)
          (replace 'install
            (lambda _
              (install-file "bitmapperBS"
                            (string-append #$output "/bin/")))))))
    (inputs
     (list libdivsufsort psascan zlib))
    (home-page "https://github.com/chhylp123/BitMapperBS/")
    (synopsis "Read aligner for whole-genome bisulfite sequencing")
    (description
     "BitMapperBS is memory-efficient aligner that is designed for
whole-genome bisulfite sequencing (WGBS) reads from directional protocol.")
    (supported-systems '("x86_64-linux"))
    (license license:asl2.0)))

(define-public bustools
  (package
    (name "bustools")
    (version "0.43.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BUStools/bustools")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "068kjlc4d528269nl5mc3j8h2c95r1v545d3fi1iw1ckg8rba0hg"))))
    (build-system cmake-build-system)
    (arguments (list #:tests? #f))          ;no test target
    (inputs (list zlib))
    (home-page "https://bustools.github.io")
    (synopsis "Tools for working with BUS files")
    (description "bustools is a program for manipulating BUS files for single
cell RNA-Seq datasets.  It can be used to error correct barcodes, collapse
UMIs, produce gene count or transcript compatibility count matrices, and is useful
for many other tasks.")
    (license license:bsd-2)))

(define-public cellsnp-lite
  ;; Last release is from November 2021 and does not contain fixes.
  (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a")
        (revision "0"))
    (package
      (name "cellsnp-lite")
      (version (git-version "1.2.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/single-cell-genetics/cellsnp-lite")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444"))))
      (build-system gnu-build-system)
      (arguments
       (list
        #:configure-flags
        #~(list (string-append "--with-htslib="
                               #$(this-package-input "htslib")))))
      (inputs
       (list curl
             htslib
             openssl
             zlib))
      (native-inputs
       (list autoconf))
      (home-page "https://cellsnp-lite.readthedocs.io")
      (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data")
      (description
       "This package is designed to pileup the expressed alleles in
single-cell or bulk RNA-seq data, which can be directly used for donor
deconvolution in multiplexed single-cell RNA-seq data, particularly with other
packages, which assigns cells to donors and detects doublets as vireo, even
without genotyping reference.

This package is the C version of the deprecated cellSNP implemented in Python.
Compared to cellSNP, this package is more efficient with higher speed and less
memory usage.")
      (license license:asl2.0))))

(define-public cpat
  (package
    (name "cpat")
    (version "3.0.4")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "CPAT" version))
              (sha256
               (base32
                "0dfrwwbhv1n4nh2a903d1qfb30fgxgya89sa70aci3wzf8h2z0vd"))
              (modules '((guix build utils)))
              (snippet
               '(for-each delete-file-recursively
                          (list ".eggs"
                                "lib/__pycache__/"
                                "lib/cpmodule/__pycache__/")))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (with-directory-excursion "test"
                 ;; There is no test4.fa
                 (substitute* "test.sh"
                   ((".*-g test4.fa.*") ""))
                 (invoke "bash" "test.sh"))))))))
    (propagated-inputs
     (list python-numpy python-pysam))
    (inputs
     (list r-minimal))
    (home-page "https://wlcb.oit.uci.edu/cpat/")
    (synopsis "Alignment-free distinction between coding and noncoding RNA")
    (description
     "CPAT is a method to distinguish coding and noncoding RNA by using a
logistic regression model based on four pure sequence-based, linguistic
features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias.
Linguistic features based method does not require other genomes or protein
databases to perform alignment and is more robust.  Because it is
alignment-free, it runs much faster and also easier to use.")
    (license license:gpl2+)))

(define-public pbcopper
  (package
    (name "pbcopper")
    (version "2.0.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/PacificBiosciences/pbcopper")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "04mgmla96bsmr9gijbn3ibspry625cv4kqqxv70z4jq4qc407jy3"))))
    (build-system meson-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-meson-files
           (lambda _
             (substitute* "meson.build"
               (("-msse4.1") "")))))))
    (inputs
     (list boost))
    (native-inputs
     (list googletest pkg-config))
    (home-page "https://github.com/PacificBiosciences/pbcopper")
    (synopsis "Data structures, algorithms, and utilities for PacBio C++ applications")
    (description
     "The pbcopper library provides a suite of data structures, algorithms,
and utilities for PacBio C++ applications.")
    (license license:bsd-3)))

(define-public r-anndatar
  (let ((commit "5c3eb7e498d0d9bf1c522ad66f4eb8ad277238b6")
        (revision "1"))
    (package
      (name "r-anndatar")
      (version (git-version "0.99.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/scverse/anndataR")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0sx87i8cb4p08ihgpgflxs0fhkr1kw6lxvky4w766rq7wqy41cgk"))))
      (properties `((upstream-name . "anndataR")))
      (build-system r-build-system)
      (propagated-inputs (list r-matrix r-r6))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/scverse/anndataR")
      (synopsis "AnnData interoperability in R")
      (description
       "This package aims to bring the power and flexibility of @code{AnnData}
to the R ecosystem, allowing you to effortlessly manipulate and analyze your
single-cell data.  This package lets you work with backed h5ad and zarr files,
directly access various slots (e.g. X, obs, var), or convert the data into
@code{SingleCellExperiment} and Seurat objects.")
      (license license:expat))))

(define-public r-anpan
  (let ((commit "286b88dcf5e9e963a595482139aade154ee1dc86")
        (revision "1"))
    (package
      (name "r-anpan")
      (version (git-version "0.3.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/biobakery/anpan")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "10nw5v69gn4pxb4g5gd8nh9r1ywd6yczapl3dpdfms0434wcmkxm"))))
      (properties `((upstream-name . "anpan")))
      (build-system r-build-system)
      (propagated-inputs (list r-ape
                               r-cmdstanr
                               r-data-table
                               r-dplyr
                               r-fastglm
                               r-furrr
                               r-future
                               r-ggdendro
                               r-ggnewscale
                               r-ggplot2
                               r-loo
                               r-mass
                               r-patchwork
                               r-phylogram
                               r-posterior
                               r-progressr
                               r-purrr
                               r-r-utils
                               r-stringr
                               r-tibble
                               r-tidyselect))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/biobakery/anpan")
      (synopsis "Quantifying microbial strain-host associations")
      (description
       "The goal of anpan is to consolidate statistical methods for strain
analysis.  This includes automated filtering of metagenomic functional
profiles, testing genetic elements for association with outcomes, phylogenetic
association testing, and pathway-level random effects models.")
      (license license:expat))))

(define-public r-bedtorch
  (let ((commit "f5ff4f83b94f59eac660333c64e4b2f296b35cea")
        (revision "1"))
    (package
      (name "r-bedtorch")
      (version (git-version "0.1.12.12" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/haizi-zh/bedtorch/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "08l04iqf54b5995gc7rvqqd7w327fwqs7qjyhc9y5cqfj8yv4c48"))))
      (properties `((upstream-name . "bedtorch")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-assertthat
             r-curl
             r-data-table
             r-dplyr
             r-genomeinfodb
             r-genomicranges
             r-purrr
             r-r-utils
             r-rcpp
             r-rcurl
             r-readr
             r-rhtslib12
             r-s4vectors
             r-stringr
             r-tidyr))
      (home-page "https://github.com/haizi-zh/bedtorch/")
      (synopsis "R package for fast BED-file manipulation")
      (description
       "The goal of bedtorch is to provide a fast BED file manipulation tool
suite native in R.")
      (license license:expat))))

(define-public r-bpcells
  (let ((commit "32ce67312185d3ed1046b4218dd3aaf1b35dcfda")
        (revision "1"))
    (package
      (name "r-bpcells")
      (version (git-version "0.1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/bnprks/BPCells/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0im4sqvbii326acmd1hnimyzsllnbvnh9al3dp1nla6isgi7s6cg"))))
      (properties `((upstream-name . "BPCells")))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'do-not-tune
             (lambda _
               (substitute* "configure"
                 (("\"-march=native\"") "\"\"")))))))
      (inputs (list hdf5 zlib))
      (propagated-inputs (list r-dplyr
                               r-ggplot2
                               r-ggrepel
                               r-hexbin
                               r-magrittr
                               r-matrix
                               r-patchwork
                               r-rcolorbrewer
                               r-rcpp
                               r-rcppeigen
                               r-rlang
                               r-scales
                               r-scattermore
                               r-stringr
                               r-tibble
                               r-tidyr
                               r-vctrs))
      (native-inputs (list pkg-config))
      (home-page "https://github.com/bnprks/BPCells/")
      (synopsis "Single cell counts matrices to PCA")
      (description
       "This is a package providing efficient operations for single cell
ATAC-seq fragments and RNA counts matrices.  It is interoperable with standard
file formats, and introduces efficient bit-packed formats that allow large
storage savings and increased read speeds.")
      (license license:gpl3))))

(define-public r-btools
  (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5")
        (revision "1"))
    (package
      (name "r-btools")
      (version (git-version "0.0.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/twbattaglia/btools")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0bca593dnxz6xdywpdi0ipli0paln2b3bfxxj0csnmj55ryrz428"))))
      (properties `((upstream-name . "btools")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biomformat
             r-coin
             r-deseq2
             r-dplyr
             r-genefilter
             r-phyloseq
             r-picante
             r-plotly
             r-reshape2
             r-stringr
             r-vegan))
      (home-page "https://github.com/twbattaglia/btools")
      (synopsis "R functions for microbial diversity analyses")
      (description
       "This package provides an assortment of R functions that is suitable
for all types of microbial diversity analyses.")
      (license license:expat))))

(define-public r-codeandroll2
  (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f")
        (revision "1"))
    (package
      (name "r-codeandroll2")
      (version (git-version "2.3.6" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/CodeAndRoll2")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71"))))
      (properties `((upstream-name . "CodeAndRoll2")))
      (build-system r-build-system)
      (propagated-inputs (list r-colorramps
                               r-dplyr
                               r-gplots
                               r-gtools
                               r-plyr
                               r-rcolorbrewer
                               r-sessioninfo
                               r-sm
                               r-stringendo
                               r-stringr))
      (home-page "https://github.com/vertesy/CodeAndRoll2")
      (synopsis "CodeAndRoll2 for vector, matrix and list manipulations")
      (description
       "CodeAndRoll2 is a set of more than 130 productivity functions.
These functions are used by MarkdownReports, ggExpress, and SeuratUtils.")
      (license license:gpl3))))

(define-public r-conospanel
  (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9")
        (revision "1"))
    (package
      (name "r-conospanel")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/kharchenkolab/conosPanel")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1zf0aj5d4iaxc3ghvjnaja5qby1avlmljzh94bpyvxbd359z9snn"))))
      (properties `((upstream-name . "conosPanel")))
      (build-system r-build-system)
      (home-page "https://github.com/kharchenkolab/conosPanel")
      (synopsis "Data for the conos package")
      (description "The data within this package is a panel of four samples,
each with 3000 cells.  There are two samples which are bone marrow (BM), and
two samples which are cord blood (CB).")
      (license license:gpl3))))

(define-public r-conqur
  (let ((commit "c7a88794efd4ecfe4d96988dceeec3b410222e48")
        (revision "1"))
    (package
      (name "r-conqur")
      (version (git-version "2.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/wdl2459/ConQuR")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "19a7p2l67mgjy99i5ksjxlhzaqmrnyi1vzvwnhgnx2jrr6crj7rq"))))
      (properties `((upstream-name . "ConQuR")))
      (build-system r-build-system)
      (propagated-inputs (list r-ade4
                               r-ape
                               r-compositions
                               r-cqrreg
                               r-doparallel
                               r-dplyr
                               r-fastdummies
                               r-glmnet
                               r-gplots
                               r-gunifrac
                               r-quantreg
                               r-randomforest
                               r-rocr
                               r-vegan))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/wdl2459/ConQuR")
      (synopsis "Batch effects removal for microbiome data")
      (description
       "This package conducts batch effects removal from a taxa read count
table by a conditional quantile regression method.  The distributional
attributes of microbiome data - zero-inflation and over-dispersion, are
simultaneously considered.")
      (license license:gpl3))))

(define-public r-ewastools
  (let ((commit "f7646cacd73266708479b3fea5d625054d179f95")
        (revision "1"))
    (package
      (name "r-ewastools")
      (version (git-version "1.7.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/hhhh5/ewastools/")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0irarlnxfnasa755adxsn67rxsy01zwhjhw18g4cag08cqiyyw41"))))
      (properties `((upstream-name . "ewastools")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-data-table
             r-igraph
             r-illuminaio
             r-mblm
             r-quadprog))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/hhhh5/ewastools/")
      (synopsis
       "Quality control toolset for the Illumina Infinium DNA methylation")
      (description
       "This package provides a collection of useful functions for working
with DNA methylation micro-array data.")
      (license license:unlicense))))

(define-public r-hdwgcna
  (let ((commit "950b8c74c5d74b30b4a562820e70ca00ee29e2c6")
        (revision "1"))
    (package
      (name "r-hdwgcna")
      (version (git-version "0.4.00" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/smorabit/hdWGCNA")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0d9hr2ly7k6kq6yp5spjlp6lp9yx593xmggajyzjxlhxi2lbyqgn"))
         (snippet
          '(for-each delete-file
                     (list
                      "docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js"
                      "docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"
                      "docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"
                      "docs/deps/clipboard.js-2.0.11/clipboard.min.js"
                      "docs/deps/headroom-0.11.0/headroom.min.js"
                      "docs/deps/headroom-0.11.0/jQuery.headroom.min.js"
                      "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js"
                      "docs/deps/search-1.0.0/autocomplete.jquery.min.js"
                      "docs/deps/search-1.0.0/fuse.min.js"
                      "docs/deps/search-1.0.0/mark.min.js")))))
      (properties `((upstream-name . "hdWGCNA")))
      (build-system r-build-system)
      (arguments
       (list
        #:modules
        '((guix build r-build-system)
          (guix build minify-build-system)
          (guix build utils)
          (ice-9 match))
        #:imported-modules
        `(,@%r-build-system-modules (guix build minify-build-system))
        #:phases
        '(modify-phases (@ (guix build r-build-system) %standard-phases)
           (add-after 'unpack 'process-javascript
             (lambda* (#:key inputs #:allow-other-keys)
               (with-directory-excursion "docs/deps/"
                 (for-each (match-lambda
                             ((source . target)
                              (minify source #:target target)))
                           `((,(string-append (assoc-ref inputs "js-bootstrap-5.1")
                                              "/dist/js/bootstrap.bundle.js")
                              . "bootstrap-5.1.0/bootstrap.bundle.min.js")
                             (,(string-append (assoc-ref inputs "js-bootstrap-5.3")
                                              "/dist/js/bootstrap.bundle.js")
                              . "bootstrap-5.3.1/bootstrap.bundle.min.js")
                             (,(search-input-file inputs "/dist/bootstrap-toc.js")
                              . "bootstrap-toc-1.0.1/bootstrap-toc.min.js")
                             (,(search-input-file inputs "/dist/clipboard.js")
                              . "clipboard.js-2.0.11/clipboard.min.js")
                             ("jquery-3.6.0/jquery-3.6.0.js"
                              . "jquery-3.6.0/jquery-3.6.0.min.js")
                             (,(search-input-file inputs "/dist/autocomplete.jquery.js")
                              . "search-1.0.0/autocomplete.jquery.min.js")
                             (,(search-input-file inputs "/dist/fuse.js")
                              . "search-1.0.0/fuse.min.js")
                             (,(search-input-file inputs "/dist/mark.js")
                              . "search-1.0.0/mark.min.js")
                             (,(assoc-ref inputs "js-headroom")
                              . "headroom-0.11.0/headroom.min.js")
                             (,(assoc-ref inputs "js-headroom-jquery")
                              . "docs/deps/headroom-0.11.0/jQuery.headroom.min.js")))))))))
      (propagated-inputs (list r-dplyr
                               r-enrichr
                               r-geneoverlap
                               r-genomicranges
                               r-ggplot2
                               r-ggraph
                               r-ggrepel
                               r-harmony
                               r-igraph
                               r-matrix
                               r-proxy
                               r-seurat
                               r-tester
                               r-tidygraph
                               r-ucell
                               r-wgcna))
      (native-inputs
       `(("esbuild" ,esbuild)
         ("js-autocomplete"
          ,(let ((version "0.38.0"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/algolia/autocomplete")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-autocomplete" version))
               (sha256
                (base32
                 "04r1qmd5cxcf8cf471kx51y6wq86rh54y42y7xl51z95ag5csswl")))))
         ("js-bootstrap-5.1"
          ,(let ((version "5.1.0"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/twbs/bootstrap")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-bootstrap" version))
               (sha256
                (base32
                 "0wjyi497wy2lbypkxwa72z294zbh827lb2s8pzgi40hvjsw00ns4")))))
         ("js-bootstrap-5.3"
          ,(let ((version "5.3.1"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/twbs/bootstrap")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-bootstrap" version))
               (sha256
                (base32
                 "045majqayd4wrpq3r3fisi56grwizykwj5705jlzsg7bwln8v3qr")))))
         ("js-bootstrap-toc"
          ,(let ((version "1.0.1"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/afeld/bootstrap-toc")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-bootstrap-toc" version))
               (sha256
                (base32
                 "1d4rqvbkwmmld0d8nz2is1rwc55rlb4b0v2anylxj63335cs0mk0")))))
         ("js-clipboard"
          ,(let ((version "2.0.11"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/zenorocha/clipboard.js")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-clipboard" version))
               (sha256
                (base32
                 "0nn9cry7ddf47vkl3vnpc4z86da46wq7m3qf3awcs05197bjn1vj")))))
         ("js-fuse"
          ,(let ((version "6.4.6"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/krisk/Fuse")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-fuse" version))
               (sha256
                (base32
                 "1k0l2vxw4nsmwrz48kmgv41ymphrdwbdbckiv9w011jwbnfsqvn5")))))
         ("js-mark"
          ,(let ((version "8.11.1"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/julkue/mark.js")
                     (commit version)))
               (file-name (git-file-name "js-mark" version))
               (sha256
                (base32
                 "108cw4732wjlwwjwpc86fqlr8yfrlagqdn7126qxa70c0ldfma93")))))
         ("js-headroom"
          ,(let ((version "0.11.0"))
             (origin
               (method url-fetch)
               (uri (string-append "https://unpkg.com/headroom.js@"
                                   version "/dist/headroom.js"))
               (file-name (string-append "js-headroom-" version ".js"))
               (sha256
                (base32
                 "0d76fpajxzwsj4847zgrv05daq8ri8hcww5dcldq1q2iyyxsmrva")))))
         ("js-headroom-jquery"
          ,(let ((version "0.11.0"))
             (origin
               (method url-fetch)
               (uri (string-append "https://unpkg.com/headroom.js@"
                                   version "/dist/jQuery.headroom.js"))
               (file-name (string-append "js-headroom-jquery-" version ".js"))
               (sha256
                (base32
                 "1jz1ampd9k8p32m6bid4yrr66bkngd8blj2q0774hl91rszhjqrv")))))))
      (home-page "https://github.com/smorabit/hdWGCNA")
      (synopsis "Weighted gene co-expression network analysis")
      (description
       "@code{hdWGCNA} is an R package for performing weighted gene
co-expression network analysis in high dimensional -omics such as single-cell
RNA-seq or spatial transcriptomics.")
      (license license:gpl3))))

(define-public r-netid
  (let ((commit "6ad1ffdd64a6584cc1d392524dad8e248d4590a8")
        (revision "1"))
    (package
      (name "r-netid")
      (version (git-version "0.1.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/WWXkenmo/NetID_package")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1blm5ljql91xmbyxxwm3vw8iz8d4ir9gm7wfnapqhfdbjvg4l21q"))))
      (properties `((upstream-name . "NetID")))
      (build-system r-build-system)
      (propagated-inputs (list r-doparallel
                               r-dorng
                               r-glmnet
                               r-hmisc
                               r-igraph
                               r-irlba
                               r-lmtest
                               r-matrix
                               r-mclust
                               r-pracma
                               r-raceid
                               r-rarpack
                               r-reticulate
                               r-robustrankaggreg
                               r-rsvd
                               r-seurat))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/WWXkenmo/NetID_package")
      (synopsis
       "Scalable method to infer fate-specific networks from single-cell data")
      (description
       "This package provides a method to sample cells from single-cell data.
It also generates an aggregate profile on a pruned K-Nearest Neighbor graph.
This approach leads to an improved gene expression profile for quantifying
gene regulations.")
      (license license:expat))))

(define-public r-numbat
  (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295")
        (revision "1"))
    (package
      (name "r-numbat")
      (version (git-version "1.3.2-1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/kharchenkolab/numbat")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0wa2cz5iy570r2a57bd74jramxayvfhmxznb0vq4vyk1ia8l5jd1"))))
      (properties `((upstream-name . "numbat")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-ape
             r-catools
             r-data-table
             r-dendextend
             r-dplyr
             r-genomicranges
             r-ggplot2
             r-ggraph
             r-ggtree
             r-glue
             r-igraph
             r-iranges
             r-logger
             r-magrittr
             r-matrix
             r-optparse
             r-paralleldist
             r-patchwork
             r-pryr
             r-purrr
             r-r-utils
             r-rcpp
             r-rcpparmadillo
             r-rhpcblasctl
             r-roptim
             r-scales
             r-scistreer
             r-stringr
             r-tibble
             r-tidygraph
             r-tidyr
             r-vcfr
             r-zoo))
      (home-page "https://github.com/kharchenkolab/numbat")
      (synopsis "Haplotype-Aware CNV Analysis from scRNA-Seq")
      (description
       "This package provides a computational method that infers copy number
variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor
phylogeny.  numbat integrates signals from gene expression, allelic ratio, and
population haplotype structures to accurately infer allele-specific CNVs in
single cells and reconstruct their lineage relationship.  numbat can be used
to:

@enumerate
@item detect allele-specific copy number variations from single-cells;
@item differentiate tumor versus normal cells in the tumor microenvironment;
@item infer the clonal architecture and evolutionary history of profiled
tumors.
@end enumerate

numbat does not require tumor/normal-paired DNA or genotype data, but operates
solely on the donor scRNA-data data (for example, 10x Cell Ranger output).")
      (license license:expat))))

(define-public r-p2data
  (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c")
        (revision "1"))
    (package
      (name "r-p2data")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/kharchenkolab/p2data")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1hadrldldxvhqs43aqs3c88bqfgql3wcfkbll3jz7fh6z7p3x324"))))
      (properties `((upstream-name . "p2data")))
      (build-system r-build-system)
      (home-page "https://github.com/kharchenkolab/p2data")
      (synopsis "Data for pagoda2")
      (description "This package contains data used by pagoda2.  The data
within this package are the 3000 bone marrow cells used for vignettes.")
      (license license:gpl3))))

(define-public r-rhtslib12
  (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
        (revision "1"))
    (package
      (name "r-rhtslib12")
      (version (git-version "1.23.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/haizi-zh/Rhtslib12")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0a3kkp0phi2fq6ip8p9vfj3axn7l15f2mb51a6v3ai4nlkhqqawj"))))
      (properties `((upstream-name . "Rhtslib12")))
      (build-system r-build-system)
      (propagated-inputs (list curl zlib r-zlibbioc))
      (native-inputs (list pkg-config r-knitr))
      (home-page "https://github.com/haizi-zh/Rhtslib12")
      (synopsis "HTSlib high-throughput sequencing library as an R package")
      (description
       "This package provides version 1.12 of the HTSlib C library for
high-throughput sequence analysis.  The package is primarily useful to
developers of other R packages who wish to make use of HTSlib.")
      (license license:lgpl2.0+))))

(define-public r-scdesign2
  (let ((commit "554f2c4b1a7ee6cc04969a287df9b3b77d7bb2fe")
        (revision "1"))
    (package
      (name "r-scdesign2")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/JSB-UCLA/scDesign2")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "09zkz6qdcx54092ab6761ja3pclax9xzana8dk8qvxrdbjshb8p7"))))
      (properties `((upstream-name . "scDesign2")))
      (build-system r-build-system)
      (propagated-inputs (list r-mass r-pscl))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/JSB-UCLA/scDesign2")
      (synopsis "Statistical simulator for scRNA-seq with gene correlation")
      (description
       "This package offers a flexible statistical simulator for scRNA-seq data.
It can generate data that captures gene correlation.  Additionally, it allows
for varying the number of cells and sequencing depth.")
      (license license:expat))))

(define-public r-scenic
  (let ((commit "cedf8490a634da550cea2c831544e5f7f14467d2")
        (revision "1"))
    (package
      (name "r-scenic")
      (version (git-version "1.3.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/aertslab/SCENIC")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "17ai0q260hdqbvm1km1s5dw93pgz4f546ycfii57jyy9m9jka7r0"))))
      (properties `((upstream-name . "SCENIC")))
      (build-system r-build-system)
      (propagated-inputs (list r-aucell
                               r-data-table
                               r-dynamictreecut
                               r-genie3
                               r-ggrepel
                               r-mixtools
                               r-nmf
                               r-rcistarget
                               r-rtsne))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/aertslab/SCENIC")
      (synopsis
       "SCENIC (Single Cell rEgulatory Network Inference and Clustering)")
      (description "SCENIC (Single-cell regulatory network inference and
clustering) is an R package to infer Gene Regulatory Networks and cell types
from single-cell RNA-seq data.")
      ;; As of commit cedf8490a634da550cea2c831544e5f7f14467d2 the license is
      ;; GPLv3.
      (license license:gpl3))))

(define-public r-scent
  (let ((commit "f01f18ac30f8a9bcf85b738c6c7815017e2c8ee5")
        (revision "1"))
    (package
      (name "r-scent")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/immunogenomics/SCENT")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "18krksy8ac7yy8hghzaxscj91c61j195yg7j60zswdq97islvfzi"))))
      (properties `((upstream-name . "SCENT")))
      (build-system r-build-system)
      (inputs (list bedtools))
      (propagated-inputs (list r-boot
                               r-data-table
                               r-hmisc
                               r-lme4
                               r-mass
                               r-matrix
                               r-r-utils
                               r-stringr))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/immunogenomics/SCENT")
      (synopsis
       "Single-Cell enhancer target gene mapping for multimodal single-cell data")
      (description
       "This package contains functions for the SCENT algorithm.
SCENT uses single-cell multimodal data and links ATAC-seq peaks
to their target genes by modeling association between chromatin
accessibility and gene expression across individual single cells.")
      (license license:expat))))

(define-public r-saige
  (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167")
        (revision "1"))
    (package
      (name "r-saige")
      (version (git-version "1.3.4" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/saigegit/SAIGE")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0c3211whqazycs9ivwdz23imj45j4na2xzcfq5l989ykkgmqnjzs"))))
      (properties `((upstream-name . "SAIGE")))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'do-not-download-packages
             (lambda _
               ;; Pretend to be a Conda build to avoid having to install
               ;; things with pip and cget.
               (setenv "CONDA_BUILD" "1")))
           (add-after 'unpack 'link-with-openblas
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* "src/Makevars"
                 (("-llapack")
                  (search-input-file inputs
                                     "/lib/libopenblas.so"))))))))
      (inputs (list openblas savvy superlu zlib zstd))
      (propagated-inputs (list r-bh
                               r-data-table
                               r-dplyr
                               r-matrix
                               r-metaskat
                               r-optparse
                               r-qlcmatrix
                               r-rcpp
                               r-rcpparmadillo
                               r-rcppeigen
                               r-rcppparallel
                               r-rhpcblasctl
                               r-rsqlite
                               r-skat
                               r-spatest))
      (home-page "https://github.com/saigegit/SAIGE")
      (synopsis "Genome-wide association tests in large-scale data sets")
      (description "SAIGE is a package for efficiently controlling for
case-control imbalance and sample relatedness in single-variant assoc
tests (SAIGE) and controlling for sample relatedness in region-based assoc
tests in large cohorts and biobanks (SAIGE-GENE+).")
      (license license:gpl2+))))

(define-public r-singlet
  (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36")
        (revision "1"))
    (package
      (name "r-singlet")
      (version (git-version "0.99.26" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/zdebruine/singlet")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "040v8wzl9qr8ribr6qss61fz4698d14cqs8nxbc8hqwiqlpy3vs4"))))
      (properties `((upstream-name . "singlet")))
      (build-system r-build-system)
      (propagated-inputs (list r-dplyr
                               r-fgsea
                               r-ggplot2
                               r-knitr
                               r-limma
                               r-matrix
                               r-msigdbr
                               r-rcpp
                               r-rcppml/devel
                               r-reshape2
                               r-scuttle
                               r-seurat))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/zdebruine/singlet")
      (synopsis "Non-negative Matrix Factorization for single-cell analysis")
      (description
       "This is a package for fast @dfn{Non-negative Matrix
Factorization} (NMF) with automatic rank-determination for dimension reduction
of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and
similar.")
      (license license:gpl2+))))

(define-public r-stacas
  (package
    (name "r-stacas")
    (version "2.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/carmonalab/STACAS")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm"))))
    (properties `((upstream-name . "STACAS")))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biocneighbors
           r-biocparallel
           r-ggplot2
           r-ggridges
           r-pbapply
           r-r-utils
           r-seurat))
    (home-page "https://github.com/carmonalab/STACAS")
    (synopsis "Sub-type anchoring correction for alignment in Seurat")
    (description
     "This package implements methods for batch correction and integration of
scRNA-seq datasets, based on the Seurat anchor-based integration framework.
In particular, STACAS is optimized for the integration of heterogenous
datasets with only limited overlap between cell sub-types (e.g. TIL sets of
CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default
Seurat alignment methods would tend to over-correct biological differences.
The 2.0 version of the package allows the users to incorporate explicit
information about cell-types in order to assist the integration process.")
    (license license:gpl3)))

(define-public r-stringendo
  (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a")
        (revision "1"))
    (package
      (name "r-stringendo")
      (version (git-version "0.6.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/Stringendo")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "15ij4zf2j9c8m9n4bqhmxkchjh2bhddwjfxngfpwv7c5wjqyi6ir"))))
      (properties `((upstream-name . "Stringendo")))
      (build-system r-build-system)
      (propagated-inputs (list r-clipr))
      (home-page "https://github.com/vertesy/Stringendo")
      (synopsis "Stringendo is a string parsing library")
      (description
       "This package provides string parsing functionalites for generating
plotnames, filenames and paths.")
      (license license:gpl3))))

(define-public r-readwriter
  (let ((commit "91373c44641014a1ce8e1c3e928747608aae8f54")
        (revision "1"))
    (package
      (name "r-readwriter")
      (version (git-version "1.5.3" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/ReadWriter")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "156kvmplrip0w1zhs9yl5r0ayjipa0blhy614l65hbsjn1lwbskr"))))
      (properties `((upstream-name . "ReadWriter")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-gtools r-openxlsx r-readr r-stringendo))
      (home-page "https://github.com/vertesy/ReadWriter")
      (synopsis "Functions to read and write files conveniently")
      (description
       "ReadWriter is a set of R functions to read and write files
conveniently.")
      (license license:gpl3))))

(define-public r-streamgraph
  (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb")
        (revision "1"))
    (package
      (name "r-streamgraph")
      (version (git-version "0.9.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/hrbrmstr/streamgraph")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "010rhnby5a9dg08jvlkr65b3p9iipdxi2f5m1k6j53s80p25yvig"))))
      (properties `((upstream-name . "streamgraph")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-dplyr
             r-htmltools
             r-htmlwidgets
             r-magrittr
             r-tidyr
             r-xts))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/hrbrmstr/streamgraph")
      (synopsis "Htmlwidget for building streamgraph visualizations")
      (description
       "A streamgraph is a type of stacked area chart.  It represents the
evolution of a numeric variable for several groups.  Areas are usually
displayed around a central axis, and edges are rounded to give a flowing
shape.  This package provides an @code{htmlwidget} for building streamgraph
visualizations.")
      (license license:expat))))

(define-public r-wasabi
  (let ((commit "8c33cabde8d18c2657cd6e38e7cb834f87cf9846")
        (revision "1"))
    (package
      (name "r-wasabi")
      (version (git-version "1.0.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/COMBINE-lab/wasabi")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0rpdj6n4cnx8n2zl60dzgl638474sg49dknwi9x3qb4g56dpphfa"))))
      (properties `((upstream-name . "wasabi")))
      (build-system r-build-system)
      (propagated-inputs (list r-data-table r-rhdf5 r-rjson))
      (home-page "https://github.com/COMBINE-lab/wasabi")
      (synopsis "Use Sailfish and Salmon with Sleuth")
      (description
       "This package converts the output of the Sailfish and Salmon RNA-seq
quantification tools so that it can be used with the Sleuth differential
analysis package.")
      (license license:bsd-3))))

(define-public pbbam
  (package
    (name "pbbam")
    (version "2.1.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/PacificBiosciences/pbbam")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1iyazi3l7dswpfxh39k5j7ydi0ywja0579xz3r6l9kkwz2n1z6dc"))))
    (build-system meson-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-tests
           (lambda* (#:key inputs #:allow-other-keys)
             ;; Disable this test.  I tried fixing it by including
             ;; optional_io.hpp, but there's a type error.
             (substitute* "tests/src/meson.build"
               (("'test_ReadGroupInfo.cpp',") ""))
             #;
             (substitute* "include/pbbam/ReadGroupInfo.h"
               (("#include <boost/optional.hpp>" m)
                (string-append m "\n#include <boost/optional/optional_io.hpp>")))
             (substitute* '("tests/scripts/cram/_test.py"
                            "tests/scripts/cram/_main.py")
               (("'/bin/sh'")
                (string-append "'" (which "sh") "'"))))))))
    ;; These libraries are listed as "Required" in the pkg-config file.
    (propagated-inputs
     (list htslib-1.14 pbcopper zlib))
    (inputs
     (list boost samtools))
    (native-inputs
     (list googletest
           pkg-config
           python-wrapper)) ;for tests
    (home-page "https://github.com/PacificBiosciences/pbbam")
    (synopsis "Work with PacBio BAM files")
    (description
     "The pbbam software package provides components to create, query, and
edit PacBio BAM files and associated indices.  These components include a core
C++ library, bindings for additional languages, and command-line utilities.
This library is not intended to be used as a general-purpose BAM utility - all
input and output BAMs must adhere to the PacBio BAM format specification.
Non-PacBio BAMs will cause exceptions to be thrown.")
    (license license:bsd-3)))

(define-public pbgzip
  (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
    (package
      (name "pbgzip")
      (version (git-version "0.0.0" "0" commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/nh13/pbgzip")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
      (build-system gnu-build-system)
      (native-inputs
       (list autoconf automake))
      (inputs
       (list zlib))
      (home-page "https://github.com/nh13/pbgzip")
      (synopsis "Parallel Block GZIP")
      (description "This package implements parallel block gzip.  For many
formats, in particular genomics data formats, data are compressed in
fixed-length blocks such that they can be easily indexed based on a (genomic)
coordinate order, since typically each block is sorted according to this order.
This allows for each block to be individually compressed (deflated), or more
importantly, decompressed (inflated), with the latter enabling random retrieval
of data in large files (gigabytes to terabytes).  @code{pbgzip} is not limited
to any particular format, but certain features are tailored to genomics data
formats when enabled.  Parallel decompression is somewhat faster, but the true
speedup comes during compression.")
      (license license:expat))))

(define-public blasr-libcpp
  (package
    (name "blasr-libcpp")
    (version "5.3.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/PacificBiosciences/blasr_libcpp")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "07cdfnfl29zf2j7fpaaqaxghq3p0wnc109razs0icwm2q6l3gycb"))))
    (build-system meson-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'link-with-hdf5
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((hdf5 (assoc-ref inputs "hdf5")))
               (substitute* "meson.build"
                 (("libblasr_deps = \\[" m)
                  (string-append
                   m
                   (format #f "cpp.find_library('hdf5', dirs : '~a'), \
cpp.find_library('hdf5_cpp', dirs : '~a'), "
                           hdf5 hdf5)))))))
         (add-after 'unpack 'find-googletest
           (lambda* (#:key inputs #:allow-other-keys)
             ;; It doesn't find gtest_main because there's no pkg-config file
             ;; for it.  Find it another way.
             (substitute* "unittest/meson.build"
               (("libblasr_gtest_dep = dependency\\('gtest_main'.*")
                (format #f "cpp = meson.get_compiler('cpp')
libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
                        (assoc-ref inputs "googletest")))))))
       ;; TODO: unittest/libblasr_unittest cannot be linked
       ;; ld: ;; unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o:
       ;; undefined reference to symbol
       ;; '_ZN7testing8internal9DeathTest6CreateEPKcPKNS0_2REES3_iPPS1_'
       ;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so:
       ;;   error adding symbols: DSO missing from command line
       #:tests? #f
       #:configure-flags '("-Dtests=false")))
    (inputs
     (list boost hdf5 htslib pbbam zlib))
    (native-inputs
     (list googletest pkg-config))
    (home-page
     (string-append "https://web.archive.org/web/20201106122415/"
                    "https://github.com/PacificBiosciences/blasr_libcpp"))
    (synopsis "Library for analyzing PacBio genomic sequences")
    (description
     "This package provides three libraries used by applications for analyzing
PacBio genomic sequences.  This library contains three sub-libraries: pbdata,
hdf and alignment.")
    (license license:bsd-3)))

(define-public blasr
  (package
    (name "blasr")
    (version "5.3.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/PacificBiosciences/blasr")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0axyd06gn2xa0p0k76fihsbxpfxvhlb18jn6bf97c0ii58r1wc0k"))))
    (build-system meson-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'link-with-hdf5
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((hdf5 (assoc-ref inputs "hdf5")))
               (substitute* "meson.build"
                 (("blasr_deps = \\[" m)
                  (string-append
                   m
                   (format #f "cpp.find_library('hdf5', dirs : '~a'), \
cpp.find_library('hdf5_cpp', dirs : '~a'), "
                           hdf5 hdf5))))))))
       ;; Tests require "cram" executable, which is not packaged.
       #:tests? #f
       #:configure-flags '("-Dtests=false")))
    (inputs
     (list boost blasr-libcpp hdf5 pbbam zlib))
    (native-inputs
     (list pkg-config))
    (home-page (string-append "https://web.archive.org/web/20210813124135/"
                              "https://github.com/PacificBiosciences/blasr"))
    (synopsis "PacBio long read aligner")
    (description
     "Blasr is a genomic sequence aligner for processing PacBio long reads.")
    (license license:bsd-3)))

(define-public randfold
  (package
    (name "randfold")
    (version "2.0.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://bioinformatics.psb.ugent.be/"
                           "supplementary_data/erbon/nov2003/downloads/"
                           "randfold-" version ".tar.gz"))
       (sha256
        (base32
         "0gqixl4ncaibrxmn25d6lm2hrw4ml2fj13nrc9q1kilsxdfi91mj"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;no tests provided
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (replace 'install
            (lambda _
              (install-file "randfold"
                            (string-append #$output "/bin")))))))
    (inputs (list eddylab-squid))
    (home-page
     "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/")
    (synopsis "Minimum free energy of folding randomization test software")
    (description "randfold computes the probability that, for a given
sequence, the @dfn{Minimum Free Energy} (MFE) of the secondary structure is
different from MFE computed with random sequences.")
    (license license:gpl2)))

(define-public ribotaper
  (package
    (name "ribotaper")
    (version "1.3.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://ohlerlab.mdc-berlin.de/"
                                  "files/RiboTaper/RiboTaper_Version_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'install 'wrap-executables
            (lambda _
              (for-each
               (lambda (script)
                 (wrap-program (string-append #$output "/bin/" script)
                   `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
               '("create_annotations_files.bash"
                 "create_metaplots.bash"
                 "Ribotaper_ORF_find.sh"
                 "Ribotaper.sh")))))))
    (inputs
     (list bash-minimal
           bedtools-2.18
           samtools-0.1
           r-minimal
           r-foreach
           r-xnomial
           r-domc
           r-multitaper
           r-seqinr))
    (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
    (synopsis "Define translated ORFs using ribosome profiling data")
    (description
     "Ribotaper is a method for defining translated @dfn{open reading
frames} (ORFs) using ribosome profiling (ribo-seq) data.  This package
provides the Ribotaper pipeline.")
    (license license:gpl3+)))

(define-public bioawk
  (package
    (name "bioawk")
    (version "1.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/lh3/bioawk")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm"))))
    (build-system gnu-build-system)
    (inputs (list zlib))
    (native-inputs (list bison))
    (arguments
     (list
      #:tests? #f ; There are no tests to run.
      ;; Bison must generate files, before other targets can build.
      #:parallel-build? #f
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)           ; There is no configure phase.
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin"))
                    (man (string-append #$output "/share/man/man1")))
                (mkdir-p man)
                (copy-file "awk.1" (string-append man "/bioawk.1"))
                (install-file "bioawk" bin)))))))
    (home-page "https://github.com/lh3/bioawk")
    (synopsis "AWK with bioinformatics extensions")
    (description "Bioawk is an extension to Brian Kernighan's awk, adding the
support of several common biological data formats, including optionally gzip'ed
BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.  It
also adds a few built-in functions and a command line option to use TAB as the
input/output delimiter.  When the new functionality is not used, bioawk is
intended to behave exactly the same as the original BWK awk.")
    (license license:x11)))

(define-public python-bcbio-gff
  (package
    (name "python-bcbio-gff")
    (version "0.6.9")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "bcbio-gff" version))
              (sha256
               (base32
                "1pm1szyxabhn8jismrj9cjhf88ajgcmm39f0cgf36iagw5qakprl"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-biopython python-six))
    (native-inputs (list python-pytest))
    (home-page "https://github.com/chapmanb/bcbb/tree/master/gff")
    (synopsis "Read and write GFF files with Biopython integration")
    (description
     "This package lets you read and write files in Generic Feature
Format (GFF) with Biopython integration.")
    (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))

(define-public python-bcbio-gff/biopython-1.73
  (hidden-package
   (package
     (inherit python-bcbio-gff)
     (propagated-inputs
      (modify-inputs (package-propagated-inputs python-bcbio-gff)
        (replace "python-biopython" python-biopython-1.73))))))

;; Note: the name on PyPi is "biofluff".
(define-public python-biofluff
  (package
    (name "python-biofluff")
    (version "3.0.4")
    ;; PyPi tarball does not contain test data.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/simonvh/fluff")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "12yvhgp72s2ygf3h07rrc852zd6q8swc41hm28mcczpsyprggxyz"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; Theses tests require internet access
      '(list "--ignore=tests/test_mirror.py"
             "-k" "not test_plots_big")
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'matplotlib-compatibility
           (lambda _
             (substitute* "fluff/plot.py"
               (("beginarrow=False, endarrow=True,") "")))))))
    (propagated-inputs
     (list htseq
           python-matplotlib
           python-numpy
           python-palettable
           python-pybedtools
           python-pybigwig
           python-pysam
           python-scikit-learn
           python-scipy))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/simonvh/fluff/")
    (synopsis "Analysis and visualization of high-throughput sequencing data")
    (description
     "Fluff is a Python package that contains several scripts to produce
pretty, publication-quality figures for next-generation sequencing
experiments.")
    (license license:expat)))

(define-public python-bulkvis
  (let ((commit "00a82a90c7e748a34af896e779d27e78a2c82b5e")
        (revision "2"))
    (package
      (name "python-bulkvis")
      (version (git-version "2.0.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/LooseLab/bulkVis")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "02blai158xyyqcg0ljzkmfa6ci05m4awrl4njvp9nwfp717xq8n0"))
                (modules '((guix build utils)))
                (snippet
                 '(substitute* '("requirements.txt"
                                 "setup.py")
                    (("tqdm~=4.46.1") "tqdm")
                    (("tornado~=6.0.4") "tornado")
                    (("pandas~=1.0.5") "pandas")
                    (("h5py~=2.10.0") "h5py")
                    ;; See below for com
                    (("bokeh~=2.1.0") "bokeh")))))
      (build-system pyproject-build-system)
      (arguments
       (list #:tests? #f                ;There are no tests
             #:phases
             '(modify-phases %standard-phases
                ;; See https://github.com/LooseLab/bulkvis/issues/58
                (add-after 'unpack 'bokeh-compatibility
                  (lambda _
                    (substitute* "bulkvis/bulkvis.py"
                      (("import importlib" m)
                       (string-append m "
from bokeh.command.subcommand import Argument
from bokeh.util.dataclasses import entries\n"))
                      (("( *)_parser.add_argument" m indent)
                       (string-append
                        (string-join (list "if isinstance(opts, Argument):\n"
                                           "  opts = dict(entries(opts))\n")
                                     indent 'prefix)
                        m))))))))
      (propagated-inputs (list python-bokeh
                               python-dill
                               python-h5py
                               python-joblib
                               python-matplotlib
                               python-numpy
                               python-pandas
                               python-plotly
                               python-readpaf
                               python-scikit-learn
                               python-scikit-image
                               python-scipy
                               python-seaborn
                               python-tornado-6
                               python-tqdm
                               python-umap-learn))
      (native-inputs (list python-pytest))
      (home-page "https://github.com/LooseLab/bulkVis")
      (synopsis "Interactive visualization of bulk RNA-seq data")
      (description
       "This is a Python package for the interactive visualization of bulk
RNA-seq data.  It provides a range of plotting functions and interactive tools
to explore and analyze bulk RNA-seq data.")
      (license license:expat))))

(define-public python-cell2cell
  (package
    (name "python-cell2cell")
    (version "0.6.8")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/earmingol/cell2cell")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1hwww0rcv8sc4k312n4d0jhbyix1jjqgv5djg25bw8127q5iym3s"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; We remove the dependency on statannotations because it
                  ;; will not work with the current version of seaborn.  See
                  ;; https://github.com/trevismd/statannotations/issues/122
                  (substitute* "cell2cell/plotting/factor_plot.py"
                    (("from statannotations.Annotator import Annotator")
                     "")
                    (("if statistical_test is not None")
                     "if False"))
                  (substitute* "setup.py"
                    (("'statannotations',") "")
                    ;; We provide version 1.0.4, which should be fine.
                    (("'gseapy == 1.0.3'") "'gseapy'")
                    ;; Using matplotlib 3.5.2 leads to this bug:
                    ;; https://github.com/earmingol/cell2cell/issues/19 but we
                    ;; can't package a different minor version of matplotlib
                    ;; and limit its use to just this package.
                    (("matplotlib >= 3.2.0,<=3.5.1") ""))))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #f                  ;There are no tests
      #:phases
      '(modify-phases %standard-phases
         ;; Numba needs a writable dir to cache functions.
         (add-before 'build 'set-numba-cache-dir
           (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs
     (list python-gseapy
           python-kneed
           python-matplotlib
           python-networkx
           python-numpy
           python-openpyxl
           python-pandas
           python-scikit-learn
           python-scipy
           python-seaborn
           python-statsmodels
           python-scanpy
           python-seaborn
           python-tensorly
           python-tqdm
           python-umap-learn
           python-xlrd))
    (home-page "https://github.com/earmingol/cell2cell")
    (synopsis "Python library for cell communication analysis")
    (description
     "Cell2cell is a Python library for cell communication analysis.
This is a method to calculate, visualize and analyze communication between
cell types.  Cell2cell is suitable for single-cell RNA sequencing
(scRNA-seq) data.")
    (license license:bsd-3)))

(define-public python-cellbender
  (package
    (name "python-cellbender")
    (version "0.2.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/broadinstitute/CellBender")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0h9d9pznffdbya631hkk7b7jwjrgx5saqssar1d42qbyvdji3hgy"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:tests? #false)) ;there are none
    (propagated-inputs
     (list python-anndata
           python-matplotlib
           python-numpy
           python-pandas
           python-pyro-ppl
           python-scikit-learn
           python-scipy
           python-sphinx
           python-sphinx-argparse
           python-sphinx-autodoc-typehints
           python-sphinx-rtd-theme
           python-sphinxcontrib-programoutput
           python-tables))
    (home-page "https://cellbender.rtfd.io/")
    (synopsis "Eliminate technical artifacts from single-cell RNA-seq data")
    (description
     "CellBender is a software package for eliminating technical artifacts
from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
    (license license:bsd-3)))

(define-public python-celltypist
  (package
    (name "python-celltypist")
    (version "1.6.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/Teichlab/celltypist")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0c42cx01zkxr0dk5f1d7q71qdi18v2smlc3wpvwyjlzplya7k2iy"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #false ;there are none
      #:phases
      '(modify-phases %standard-phases
         (add-before 'check 'set-home
           ;; The sanity check requires a HOME directory, because celltypist
           ;; wants to write settings.
           (lambda _ (setenv "HOME" "/tmp")))
         ;; Numba needs a writable dir to cache functions.
         (add-before 'build 'set-numba-cache-dir
           (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs
     (list python-click
           python-leidenalg
           python-numpy
           python-openpyxl
           python-pandas
           python-scanpy
           python-scikit-learn
           python-requests))
    (home-page "https://github.com/Teichlab/celltypist")
    (synopsis "Tool for semi-automatic cell type classification")
    (description
     "CellTypist is an automated cell type annotation tool for scRNA-seq
datasets on the basis of logistic regression classifiers optimised by the
stochastic gradient descent algorithm.  CellTypist allows for cell prediction
using either built-in (with a current focus on immune sub-populations) or
custom models, in order to assist in the accurate classification of different
cell types and subtypes.")
    (license license:expat)))

(define-public python-cmseq
  (package
    (name "python-cmseq")
    (version "1.0.4")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "CMSeq" version))
              (sha256
               (base32
                "0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #false ;there are no tests
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'patch-samtools-reference
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "cmseq/cmseq.py"
               (("'samtools'")
                (string-append "'" (search-input-file inputs "/bin/samtools") "'"))))))))
    (inputs (list samtools))
    (propagated-inputs
     (list python-bcbio-gff/biopython-1.73
           python-biopython-1.73
           python-numpy
           python-pandas
           python-pysam
           python-scipy))
    (home-page "https://github.com/SegataLab/cmseq/")
    (synopsis "Set of utilities on sequences and BAM files")
    (description
     "CMSeq is a set of commands to provide an interface to .bam files for coverage
and sequence consensus.")
    (license license:expat)))

(define-public python-cyvcf2
  (package
    (name "python-cyvcf2")
    (version "0.30.28")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/brentp/cyvcf2")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk"))
       (modules '((guix build utils)))
       (snippet
        ;; Delete bundled library
        '(delete-file-recursively "htslib"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'check 'build-extensions
            (lambda _
              ;; Cython extensions have to be built before running the tests.
              (invoke "python" "setup.py" "build_ext" "--inplace")))
          (add-after 'unpack 'fix-setup
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "setup.py"
                (("^htslib_include_dirs =.*")
                 (string-append "htslib_include_dirs = [\""
                                #$(this-package-input "htslib") "/include\"]\n"))
                (("lib_name = \"libhts.so\"")
                 (string-append "lib_name = \""
                                (search-input-file inputs "lib/libhts.so.3")
                                "\"\n")))))
          (add-before 'build 'use-system-htslib-package
            (lambda _
              (setenv "CYTHONIZE" "1")
              (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL"))))))
    (inputs (list curl htslib libdeflate openssl zlib))
    (native-inputs (list python-cython python-pytest))
    (propagated-inputs
     (list python-click
           python-coloredlogs
           python-numpy))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "Fast vcf file parsing with Cython and htslib")
    (description "Cyvcf2 is a Cython wrapper around htslib built for fast
parsing of Variant Call Format (VCF) files.")
    (license license:expat)))

(define-public python-decoupler-py
  (package
    (name "python-decoupler-py")
    (version "1.6.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/saezlab/decoupler-py")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1mqkp0i8k5hzhfnka4nc2f0phmrs0k404ynbl1lqfjzywx25y75h"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             ;; These tests require internet access
             (string-append "not test_get_resource"
                            " and not test_show_resources"
                            " and not test_get_dorothea"
                            " and not test_get_progeny"
                            " and not test_get_ksn_omnipath"
                            ;; This attempts to download things for Omnipath
                            " and not test_get_collectri"))
      #:phases
      '(modify-phases %standard-phases
         (add-before 'check 'set-home
           ;; Some tests require a home directory to be set.
           (lambda _ (setenv "HOME" "/tmp")))
         ;; Numba needs a writable dir to cache functions.
         (add-before 'build 'set-numba-cache-dir
           (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs (list python-adjusttext
                             python-anndata
                             python-ipython
                             python-matplotlib
                             python-nbsphinx
                             python-numba
                             python-numpy
                             python-numpydoc
                             python-omnipath
                             python-scanpy
                             python-scikit-learn
                             python-scipy
                             python-skranger
                             python-tqdm
                             python-typing-extensions))
    (native-inputs (list python-pytest))
    (home-page "https://github.com/saezlab/decoupler-py")
    (synopsis
     "Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
    (description
     "This package provides different statistical methods to extract
biological activities from omics data within a unified framework.")
    (license license:gpl3+)))

(define-public python-demuxem
  (package
    (name "python-demuxem")
    (version "0.1.7")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "demuxEM" version))
              (sha256
               (base32
                "1bhyxqjk44bmyd26m1smapf68wyf7252kk65i27k50dd3kswgnd6"))))
    (build-system pyproject-build-system)
    ;; There are no tests.
    (arguments (list #:tests? #false))
    (propagated-inputs
     (list python-docopt
           python-importlib-metadata
           python-numpy
           python-pandas
           python-pegasusio
           python-scikit-learn
           python-scipy
           python-seaborn))
    (native-inputs (list python-cython python-setuptools-scm))
    (home-page "https://github.com/lilab-bcb/demuxEM")
    (synopsis "Analyze cell-hashing/nucleus-hashing data")
    (description
     "This is a Python module for analyzing cell-hashing/nucleus-hashing data.
It is the demultiplexing module of Pegasus, which is used by Cumulus in the
demultiplexing step.")
    (license license:bsd-3)))

(define-public python-doubletdetection
  (package
    (name "python-doubletdetection")
    (version "4.2")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "doubletdetection" version))
              (sha256
               (base32
                "0v0a19014h4p6x8pyz1s78xn3q5w5166cysvg574z6vw79a3s9vp"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #false ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'use-poetry-core
            (lambda _
              ;; Patch to use the core poetry API.
              (substitute* "pyproject.toml"
                (("poetry.masonry.api")
                 "poetry.core.masonry.api")))))))
    (propagated-inputs
     (list python-anndata
           python-ipywidgets
           python-leidenalg
           python-vtraag-louvain
           python-matplotlib
           python-numpy
           python-pandas
           python-phenograph
           python-scanpy
           python-scipy
           python-tqdm))
    (native-inputs
     (list python-black
           python-flake8
           python-poetry-core
           python-pytest))
    (home-page "https://github.com/JonathanShor/DoubletDetection")
    (synopsis
     "This is a package to detect doublets in single-cell RNA-seq count matrices")
    (description
     "This package provides a method to detect and enable removal of doublets
from single-cell RNA-sequencing.")
    (license license:expat)))

(define-public python-harmonypy
  (package
    (name "python-harmonypy")
    (version "0.0.10")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/slowkow/harmonypy")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "15lxgncrnsx1hapfx78pvx4rjx5d48hqixdnacdy55d84myfmrym"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-numpy
                             python-pandas
                             python-scikit-learn
                             python-scipy))
    (native-inputs (list python-hatchling python-pytest))
    (home-page "https://github.com/slowkow/harmonypy")
    (synopsis "Data integration algorithm")
    (description
     "Harmony is an algorithm for integrating multiple high-dimensional
datasets with fuzzy k-means and locally linear adjustments.")
    (license license:gpl2)))

(define-public python-hclust2
  (package
    (name "python-hclust2")
    (version "1.0.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "hclust2" version))
              (sha256
               (base32
                "0v89n2g42d7jhgfs8glf06apgxx6aswp3mfisgnhm518cv8z2rwn"))))
    (build-system pyproject-build-system)
    (arguments (list #:tests? #f))      ;there are no tests
    (propagated-inputs
     (list python-matplotlib
           python-numpy
           python-pandas
           python-scipy))
    (home-page "https://github.com/SegataLab/hclust2/")
    (synopsis "Plotting heat-maps for publications")
    (description
     "Hclust2 is a handy tool for plotting heat-maps with several useful options
to produce high quality figures that can be used in publications.")
    (license license:expat)))

(define-public python-hotspotsc
  (package
    (name "python-hotspotsc")
    (version "1.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "hotspotsc" version))
       (sha256
        (base32 "1phbd49nb0ivfcgfi6yxd2masgd0v6133mki9vd5pkrhx0a7wb5d"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #false                   ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'use-poetry-core
            (lambda _
              ;; Patch to use the core poetry API.
              (substitute* "pyproject.toml"
                (("poetry.masonry.api")
                 "poetry.core.masonry.api")
                ;; Fix syntax error
                (("sphinx>") "sphinx")))))))
    (propagated-inputs (list python-anndata
                             python-importlib-metadata
                             python-ipython
                             python-matplotlib
                             python-nbsphinx
                             python-numba
                             python-numpy
                             python-pandas
                             python-pynndescent
                             python-scanpy
                             python-scikit-learn
                             python-scipy
                             python-seaborn
                             python-statsmodels
                             python-tqdm))
    (native-inputs
     (list python-poetry-core python-pytest python-sphinx))
    (home-page "https://github.com/yoseflab/hotspot")
    (synopsis
     "Identifying informative genes in a single-cell dataset")
    (description
     "Hotspot is a tool for identifying informative genes (and gene modules)
in a single-cell dataset.  Importantly, \"informative\" is decided based on
how well a gene's variation agrees with some cell metric---some similarity
mapping between cells.  Genes which are informative are those whose expression
varies in similar way among cells which are nearby in the given metric.")
    (license license:expat)))

(define-public python-htsget
  (package
   (name "python-htsget")
   (version "0.2.6")
   (source (origin
            (method url-fetch)
            (uri (pypi-uri "htsget" version))
            (sha256
             (base32
              "111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4"))))
   (build-system pyproject-build-system)
   (native-inputs
    (list python-setuptools-scm))
   (propagated-inputs
    (list python-humanize python-requests python-six))
   (home-page "https://pypi.org/project/htsget/")
   (synopsis "Python API and command line interface for the GA4GH htsget API")
   (description "This package is a client implementation of the GA4GH htsget
protocol.  It provides a simple and reliable way to retrieve genomic data from
servers supporting the protocol.")
   (license license:asl2.0)))

(define-public python-liana-py
  (package
    (name "python-liana-py")
    (version "1.1.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/saezlab/liana-py")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0f5al0v55haja91q9gd409v7q78mmp1wv9znsplsbjp6lfspjfnw"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             ;; These tests require internet access.
             (string-append "not test_generate_lr_resource"
                            " and not test_get_metalinks"
                            " and not test_get_metalinks_values"
                            " and not test_describe_metalinks"
                            " and not test_generate_nondefault_lr_resource"
                            ;; Minor accuracy difference
                            " and not test_bivar_morans_perms"
                            ;; XXX unclear failure: 'coo_matrix' object is not
                            ;; subscriptable
                            " and not test_bivar_product"
                            )
             ;; These need the optional squidpy, which we don't have yet.
             "--ignore=liana/tests/test_misty.py"
             ;; These need the optional corneto.
             "--ignore=liana/tests/test_causalnet.py")
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             ;; Don't fail the sanity check when these optional inputs aren't
             ;; available.
             (substitute* "pyproject.toml"
               (("^pre-commit =.*") ""))))
         ;; Numba needs a writable directory to cache functions.
         (add-before 'build 'set-numba-cache-dir
           (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs (list python-anndata
                             python-cell2cell
                             python-decoupler-py
                             python-hypothesis
                             python-ipykernel
                             python-ipython
                             python-mudata
                             python-nbconvert
                             python-nbsphinx
                             python-numpy
                             python-numpydoc
                             python-omnipath
                             python-pandas
                             python-plotnine
                             python-pypandoc
                             python-scipy
                             python-requests
                             python-scanpy
                             python-statsmodels
                             python-tqdm
                             tzdata))
    (native-inputs
     (list python-black
           python-poetry-core
           python-pytest
           python-pytest-cov))
    (home-page "https://github.com/saezlab/liana-py")
    (synopsis "LIANA is a ligand-receptor analysis framework")
    (description "This is a Ligand-Receptor inference framework.  The
framework enables the use of any LR method with any resources.")
    (license license:gpl3+)))

(define-public python-logomaker
  (package
    (name "python-logomaker")
    (version "0.8")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "logomaker" version))
              (sha256
               (base32
                "0v9z3ml1s7imk28hqyhrqjqg3sq0j29lx975d36n2ybdgld51iyq"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-matplotlib python-numpy python-pandas))
    (home-page "https://logomaker.readthedocs.io")
    (synopsis "Package for making Sequence Logos")
    (description "Logomaker is a Python package for generating
publication-quality sequence logos.  Logomaker can generate both standard and
highly customized logos illustrating the properties of DNA, RNA, or protein
sequences.  Logos are rendered as vector graphics embedded within native
matplotlib Axes objects, making them easy to style and incorporate into
multi-panel figures.")
    (license license:expat)))

(define-public python-magic-impute
  (package
    (name "python-magic-impute")
    (version "1.2.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/KrishnaswamyLab/MAGIC")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1yjs16vg87lcg9g16bnblg1v9sk73j6dm229lkcz0bfjlzxjhv8w"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #false ;there are none
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _ (chdir "python"))))))
    (propagated-inputs
     (list python-future
           python-graphtools
           python-matplotlib
           python-numpy
           python-pandas
           python-scikit-learn
           python-scipy
           python-tasklogger))
    (home-page "https://github.com/KrishnaswamyLab/MAGIC")
    (synopsis "Markov affinity-based graph imputation of cells")
    (description "MAGIC is an interactive tool to impute missing values in
single-cell sequencing data and to restore the structure of the data.  It also
provides data pre-processing functionality such as dimensionality reduction
and gene expression visualization.")
    (license license:gpl2+)))

(define-public python-metacells
  (package
    (name "python-metacells")
    (version "0.9.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "metacells" version))
       (sha256
        (base32 "02f63nxz6b60vl6s4n9vapaysnq1w5f3x7c179rh2rr7j2k5cf1y"))))
    #;
    (properties '((tunable? . #t)))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          ;; The package "python-igraph" has been deprecated in favor of
          ;; just "igraph".
          (add-after 'unpack 'rename-igraph
            (lambda _
              (substitute* "requirements.txt"
                (("python-igraph") "igraph"))))
          (add-after 'unpack 'do-not-tune
            (lambda _
              ;; Without this they pass -march=native to the compiler.
              (setenv "WHEEL" "1")))
          ;; Numba needs a writable dir to cache functions.
          (add-before 'check 'set-numba-cache-dir
            (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))
          (add-before 'build 'build-extensions
            (lambda _
              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
    (propagated-inputs (list python-anndata
                             python-cvxpy
                             python-fastcluster
                             python-importlib-metadata
                             python-numpy
                             python-pandas
                             python-psutil
                             python-igraph
                             python-pyyaml
                             python-scanpy
                             python-scipy
                             python-threadpoolctl
                             python-umap-learn))
    (native-inputs (list python-black
                         python-bumpversion
                         python-flake8
                         python-isort
                         python-mypy
                         python-mypy-extensions
                         python-pylint
                         python-pytest
                         python-pytest-cov
                         python-sphinx
                         python-sphinx-rtd-theme
                         python-tox
                         python-twine))
    (home-page "https://github.com/tanaylab/metacells.git")
    (synopsis "Single-cell RNA Sequencing Analysis")
    (description "The metacells package implements the improved metacell
algorithm for single-cell RNA sequencing (scRNA-seq) data analysis within the
scipy framework, and projection algorithm based on it.  The original metacell
algorithm was implemented in R.  The Python package contains various
algorithmic improvements and is scalable for larger data sets (millions of
cells).")
    (license license:expat)))

(define-public python-parabam
  (package
    (name "python-parabam")
    (version "3.0.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "parabam" version))
       (sha256
        (base32 "1cy9q3gzdawi1kilycpd7waymjmrwsg8czwycfp13g301ir9xyp3"))
       (modules '((guix build utils)))
       (snippet
        '(substitute* "setup.py"
           (("'argparse',") "")))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-numpy python-pysam))
    (home-page "https://github.com/cancerit/parabam")
    (synopsis "Parallel BAM File Analysis")
    (description "Parabam is a tool for processing sequencing files in
parallel.  It uses Python's native multiprocessing framework to apply a user
defined rule on an input file.")
    (license license:gpl3)))

(define-public python-pdbfixer
  (package
    (name "python-pdbfixer")
    (version "1.9")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/openmm/pdbfixer")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             ;; These tests fail because they require internet access.
             (string-append "not test_build_and_simulate.py"
                            " and not test_cli.py"
                            " and not test_mutate.py"))))
    (propagated-inputs (list openmm python-numpy))
    (native-inputs (list python-pytest))
    (home-page "https://github.com/openmm/pdbfixer")
    (synopsis "Application for fixing problems in Protein Data Bank")
    (description
     "PDBFixer is designed to rectify issues in Protein Data Bank files.
Its intuitive interface simplifies the process of resolving problems
encountered in PDB files prior to simulation tasks.")
    (license license:expat)))

(define-public python-peaks2utr
  (package
    (name "python-peaks2utr")
    (version "1.2.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "peaks2utr" version))
              (sha256
               (base32
                "1idp9cgwqxvryf4qqrc1xjsamfqn3jmr56kmjp2h1ysmckwmhw4v"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; These two tests fail because file names are not URLs.
      '(list "-k" "not test_annotation.py")))
    (propagated-inputs
     (list python-asgiref
           python-gffutils
           python-importlib-resources
           macs
           python-numpy
           python-psutil
           python-pybedtools
           python-pysam
           python-requests
           python-tqdm
           python-typing-extensions
           python-zipp))
    (home-page "https://github.com/haessar/peaks2utr")
    (synopsis "Python CLI for annotating three prime UTR")
    (description
     "This package provides a robust, parallelized Python CLI for annotating
three prime UTR.")
    (license license:gpl3+)))

(define-public python-pegasusio
  (package
    (name "python-pegasusio")
    (version "0.7.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pegasusio" version))
              (sha256
               (base32
                "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9"))))
    (build-system pyproject-build-system)
    ;; There are no tests.
    (arguments (list #:tests? #false))
    (propagated-inputs
     (list python-anndata
           python-docopt
           python-h5py
           python-importlib-metadata
           python-loompy
           python-natsort
           python-numpy
           python-pandas
           python-pillow
           python-scipy
           python-zarr))
    (native-inputs (list python-cython python-setuptools-scm))
    (home-page "https://github.com/lilab-bcb/pegasusio")
    (synopsis "Read or write single-cell genomics data")
    (description
     "Pegasusio is a Python package for reading or writing single-cell
genomics data.")
    (license license:bsd-3)))

(define-public python-phenograph
  (package
    (name "python-phenograph")
    (version "1.5.7")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "PhenoGraph" version))
              (sha256
               (base32
                "0nji449mzwgp1f87iknl5fmnjdkrhkfkapxvafxdw01s0jg8zcj6"))
              (modules '((guix build utils)))
              ;; Remove bundled binaries
              (snippet
               '(delete-file-recursively "phenograph/louvain"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          ;; This test can never succeed because Q_leiden is never set to
          ;; anything other than None.
          (add-after 'unpack 'disable-leiden-test
            (lambda _
              (substitute* "tests/test_cluster.py"
                (("def test_run_leiden") "def _test_run_leiden"))))
          (add-after 'unpack 'patch-louvain
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "phenograph/core.py"
                (("lpath = os.path.*")
                 (string-append "lpath = \""
                                (dirname (search-input-file inputs "/bin/community"))
                                "\"\n"))
                (("linux-(community|hierarchy|convert)" _ thing) thing)
                ;; Do not write binaries, because the unmodified "convert"
                ;; from louvain only knows how to process plain text files.
                (("with open\\(filename \\+ \".bin\", \"w\\+b\"\\) as f:")
                 "with open(filename + \".bin\", \"w+\") as f:")
                (("f.writelines\\(\\[e for t in zip\\(ij, s\\) for e in t\\]\\)")
                 "for [src, dest], weight in zip(ij, s): \
f.write(src.astype(\"str\") + ' ' + \
dest.astype(\"str\") + ' ' + \
weight.astype(\"str\") + '\\n')")))))))
    (inputs
     (list louvain))
    (propagated-inputs
     (list python-leidenalg
           python-numpy
           python-psutil
           python-scikit-learn
           python-scipy))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/dpeerlab/PhenoGraph.git")
    (synopsis "Graph-based clustering for high-dimensional single-cell data")
    (description
     "PhenoGraph is a clustering method designed for high-dimensional
single-cell data.  It works by creating a graph representing phenotypic
similarities between cells and then identifying communities in this graph.")
    (license license:expat)))

(define-public python-phylophlan
  (package
    (name "python-phylophlan")
    (version "3.0.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biobakery/phylophlan")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1wz70xzxqx2sf5flmf45m15jq027dqijfaj1r51pl50w5x6dkawx"))))
    (build-system pyproject-build-system)
    (arguments (list #:tests? #f))      ;there are no tests
    (propagated-inputs
     (list python-biopython
           python-dendropy
           python-matplotlib
           python-numpy
           python-pandas
           python-seaborn))
    (home-page "https://github.com/biobakery/phylophlan")
    (synopsis
     "Phylogenetic analysis of microbial isolates and genomes from metagenomes")
    (description
     "This package is an integrated pipeline for large-scale phylogenetic
profiling of genomes and metagenomes.  PhyloPhlAn is an accurate, rapid, and
easy-to-use method for large-scale microbial genome characterization and
phylogenetic analysis at multiple levels of resolution.  This software package
can assign both genomes and @acronym{MAGs, metagenome-assembled genomes} to
@acronym{SGBs, species-level genome bins}.  PhyloPhlAn can reconstruct
strain-level phylogenies using clade- specific maximally informative
phylogenetic markers, and can also scale to very large phylogenies comprising
>17,000 microbial species.")
    (license license:expat)))

(define-public python-pybedtools
  (package
    (name "python-pybedtools")
    (version "0.9.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pybedtools" version))
              (sha256
               (base32
                "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
    (build-system pyproject-build-system)
    (arguments
     `(#:modules ((srfi srfi-26)
                  (guix build utils)
                  (guix build python-build-system)
                  (guix build pyproject-build-system))
       ;; See https://github.com/daler/pybedtools/issues/192
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'disable-broken-tests
           (lambda _
             (substitute* "pybedtools/test/test_helpers.py"
               ;; Requires internet access.
               (("def test_chromsizes")
                "def _do_not_test_chromsizes")
               ;; Broken as a result of the workaround used in the check phase
               ;; (see: https://github.com/daler/pybedtools/issues/192).
               (("def test_getting_example_beds")
                "def _do_not_test_getting_example_beds"))
             ;; This issue still occurs on python2
             (substitute* "pybedtools/test/test_issues.py"
               (("def test_issue_303")
                "def _test_issue_303"))))
         ;; Force the Cythonization of C++ files to guard against compilation
         ;; problems.
         (add-after 'unpack 'remove-cython-generated-files
           (lambda _
             (let ((cython-sources (map (cut string-drop-right <> 4)
                                        (find-files "." "\\.pyx$")))
                   (c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
               (define (strip-extension filename)
                 (string-take filename (string-index-right filename #\.)))
               (define (cythonized? c/c++-file)
                 (member (strip-extension c/c++-file) cython-sources))
               (for-each delete-file (filter cythonized? c/c++-files)))))
         (add-after 'remove-cython-generated-files 'generate-cython-extensions
           (lambda _
             (invoke "python" "setup.py" "cythonize")))
         (replace 'check
           (lambda _
             ;; The tests need to be run from elsewhere...
             (mkdir-p "/tmp/test")
             (copy-recursively "pybedtools/test" "/tmp/test")
             (with-directory-excursion "/tmp/test"
               (invoke "pytest" "-v" "--doctest-modules")))))))
    (propagated-inputs
     (list bedtools samtools python-matplotlib python-pysam
           python-pyyaml))
    (native-inputs
     (list python-numpy
           python-pandas
           python-cython
           kentutils ; for bedGraphToBigWig
           python-six
           ;; For the test suite.
           python-pytest
           python-psutil))
    (home-page "https://pythonhosted.org/pybedtools/")
    (synopsis "Python wrapper for BEDtools programs")
    (description
     "This package is a Python wrapper for Aaron Quinlan's BEDtools programs,
which are widely used for genomic interval manipulation or \"genome algebra\".
pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
    ;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in
    ;; version 0.9.0 and the LICENSE.txt is consistent with the source code.
    ;;
    ;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are
    ;; licensed lgpl2.1+
    (license (list license:expat license:lgpl2.1+))))

(define-public python-pybio
  (let ((commit "c91fddc483da535d5097364405d76ad9b1bde07f")
        (revision "1"))
    (package
      (name "python-pybio")
      (version (git-version "0.3.12" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/grexor/pybio")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0s3n1bqp25zf5pzfsj0x1kqr6i2a6iffpb8hkjwhyvjqrxf5d9rk"))))
      (build-system pyproject-build-system)
      (arguments
       (list
        #:tests? #false                 ;There are no automated tests
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'set-home
              ;; A HOME directory is required when importing the module during
              ;; the sanity check.
              (lambda _ (setenv "HOME" "/tmp")))
            (add-after 'unpack 'adjust-requirements
              (lambda _
                ;; bs4 is an alternative name for beautifulsoup4, only used to
                ;; avoid name squatting on pypi.
                (substitute* "setup.py"
                  (("bs4") "beautifulsoup4"))))
            (add-after 'unpack 'avoid-internet-while-building
              (lambda _
                (setenv "GUIX_BUILD" "yes")
                (substitute* "pybio/__init__.py"
                  (("^pybio.core.genomes.init\\(\\)" m)
                   (string-append m
                                  "\
 if not os.getenv('GUIX_BUILD') else None"))))))))
      (propagated-inputs
       (list python-beautifulsoup4 python-numpy
             python-psutil python-pysam python-requests))
      (native-inputs (list python-pytest))
      (home-page "https://github.com/grexor/pybio")
      (synopsis "Basic genomics toolset")
      (description
       "This tool provides a Python framework to streamline genomics
operations.  It offers a direct interface to Ensembl genome assemblies and
annotations, while also accommodating custom genomes via FASTA/GTF inputs.
The primary objective of pybio is to simplify genome management.  It achieves
this by providing automatic download of Ensembl genome assemblies and
annotation, provides Python genomic feature search and sequence retrieval from
the managed genomes, STAR indexing and mapping and more.")
      (license license:gpl3+))))

(define-public python-ega-download-client
  (package
    (name "python-ega-download-client")
    (version "5.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/EGA-archive/ega-download-client")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0k9rfq2yyvfxs5sq9lsm8krp9ddx4s18hv85ikf3b37zv24kpwjk"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list
        ;; These tests fail because they require internet access.
        "--ignore=tests/functional/test_download.py"
        "--ignore=tests/functional/test_htsget.py"
        "-k"
        (string-append "not test_error_5xx"
                       " and not test_error_too_many_requests"
                       ;; Something's wrong here.  On some powerful machines
                       ;; (but not on my laptop) these fail, and tests like
                       ;; test_file_is_saved_into_an_existing_directory_which_was_specified_by_the_user
                       ;; take a *very* long time to complete.
                       ;;
                       ;; It looks like "dataset_in_fire.download" takes an
                       ;; unusually long time on those machines.  We disable
                       ;; tests that fail under these conditions.
                       " and not test_download_file"
                       " and not test_output_file_is_removed_if_md5_was_invalid"
                       " and not test_post_stats_if_download_succeeded"))
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "setup.py"
               (("==") ">=")))))))
    (propagated-inputs (list python-htsget python-psutil python-requests
                             python-tqdm python-urllib3))
    (native-inputs (list python-coverage python-pytest python-pyfakefs
                         python-responses python-mock))
    (home-page "https://github.com/EGA-archive/ega-download-client")
    (synopsis "EGA download client")
    (description "PyEGA3 is a tool for viewing and downloading files from
authorized EGA datasets.  It uses the EGA data API and has several key
features:

@itemize
@item Files are transferred over secure https connections and received
  unencrypted, so no need for decryption after download.
@item Downloads resume from where they left off in the event that the
  connection is interrupted.
@item Supports file segmenting and parallelized download of segments,
  improving overall performance.
@item After download completes, file integrity is verified using checksums.
@item Implements the GA4GH-compliant htsget protocol for download of genomic
  ranges for data files with accompanying index files.
@end itemize\n")
    (license license:asl2.0)))

(define-public python-scdamandtools
  (package
    (name "python-scdamandtools")
    (version "1.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/KindLab/scDamAndTools")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1mblw6cn5jqik6ky8cv7ry99z6jm1i4r71pzdfl398vrwbda65gd"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:tests? #f))                ;there are none
    (propagated-inputs (list python-h5py
                             python-numpy
                             python-sortedcontainers
                             python-pandas
                             python-pysam
                             python-tqdm))
    (native-inputs (list python-cython python-pytest))
    (home-page "https://github.com/KindLab/scDamAndTools")
    (synopsis "Functions for processing raw scDam&T-seq data")
    (description
     "This is a set of functions for processing raw scDam&T-seq data.
scDam&T-seq is a method to simultaneously measure protein-DNA interactions and
transcription from single cells (Rooijers et al., 2019).  It combines a
DamID-based method to measure protein-DNA interactions and an adaptation of
CEL-Seq to measure transcription.  The starting point of the workflow is raw
sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq
counts.")
    (license license:expat)))

(define-public python-snaptools
  (package
    (name "python-snaptools")
    (version "1.4.8")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "snaptools" version))
       (sha256
        (base32
         "1s5373g5jjbshh3q39zy7dlxr7nda6ksxq9d1gw46h82c4fsmfbn"))))
    (build-system pyproject-build-system)
    (arguments (list #:tests? #false)) ;there are none
    (propagated-inputs
     (list python-future
           python-h5py
           python-louvain
           python-numpy
           python-pybedtools
           python-pysam))
    (home-page "https://github.com/r3fang/SnapTools")
    (synopsis "Tools for processing snap files" )
    (description
     "@code{SnapTools} can operate on snap files the following types of
operations:

@itemize
@item index the reference genome before alignment;
@item align reads to the corresponding reference genome;
@item pre-process by convert pair-end reads into fragments, checking the
  mapping quality score, alingment and filtration;
@item create the cell-by-bin matrix.
@end itemize")
    (license license:asl2.0)))

(define-public python-telomerecat
  (package
    (name "python-telomerecat")
    (version "4.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "telomerecat" version))
       (sha256
        (base32 "16mfdqmp0j6g3h26h59334w9lqb4qihqrlzwvgznj0fiqs1rkxn2"))))
    (build-system pyproject-build-system)
    (arguments (list #:tests? #false)) ;there are none
    (propagated-inputs (list python-click python-numpy python-pandas
                             python-parabam python-pysam))
    (home-page "https://github.com/cancerit/telomerecat")
    (synopsis "Telomere computational analysis tool")
    (description "Telomerecat is a tool for estimating the average telomere
length (TL) for a paired end, whole genome sequencing (WGS) sample.

Telomerecat is adaptable, accurate and fast.  The algorithm accounts for
sequencing amplification artifacts, anneouploidy (common in cancer samples)
and noise generated by WGS.  For a high coverage WGS BAM file of around 100GB
telomerecat can produce an estimate in ~1 hour.")
    (license license:gpl3)))

(define-public python-bioframe
  (package
    (name "python-bioframe")
    (version "0.6.4")
    (source
     (origin
       (method git-fetch)
       ;; pypi version does not contain tests and requirements.txt
       (uri (git-reference
             (url "https://github.com/open2c/bioframe")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1m99hgxw4cb2x4qszb2lhp1isz57sdkqbmcgisnbqxqxkv4gba7v"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k" (string-append "not test_fetch_chromsizes"
                                 " and not test_fetch_chromsizes_local_vs_ucsc"
                                 " and not test_fetch_centromeres"))
      #:phases
      '(modify-phases %standard-phases
         (add-before 'check 'pre-check
           (lambda _ (setenv "MPLCONFIGDIR" "/tmp"))))))
    (native-inputs
     (list python-biopython
           python-hatchling
           python-pysam
           python-pytest
           python-wheel))
    (propagated-inputs
     (list python-matplotlib
           python-numpy
           python-pandas
           python-pyyaml
           python-requests))
    (home-page "https://github.com/open2c/bioframe")
    (synopsis "Pandas utilities for tab-delimited and other genomic files")
    (description
     "This package is a library to enable flexible and scalable operations on
genomic interval dataframes in Python.  Bioframe enables access to a rich set
of dataframe operations.  Working in Python enables rapid visualization and
iteration of genomic analyses.  The philosophy underlying bioframe is to
enable flexible operations.  Instead of creating a function for every possible
use-case, we encourage users to compose functions to achieve their goals.")
    (license license:expat)))

(define-public python-biom-format
  (package
    (name "python-biom-format")
    (version "2.1.12")
    (source
     (origin
       (method git-fetch)
       ;; Use GitHub as source because PyPI distribution does not contain
       ;; test data: https://github.com/biocore/biom-format/issues/693
       (uri (git-reference
             (url "https://github.com/biocore/biom-format")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
       (modules '((guix build utils)))
       ;; Delete generated C files.
       (snippet
        '(for-each delete-file (find-files "." "\\.c")))))
    (build-system python-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'use-cython
           (lambda _ (setenv "USE_CYTHON" "1")))
         (add-after 'unpack 'pandas-compatibility
           (lambda _
             (substitute* "biom/tests/test_table.py"
               (("import pandas.util.testing")
                "import pandas.testing"))))
         (add-after 'unpack 'disable-broken-tests
           (lambda _
             (substitute* "biom/tests/test_util.py"
               (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
                (string-append indent
                               "@npt.dec.skipif(True, msg='Guix')\n"
                               m)))
             (substitute* "biom/tests/test_table.py"
               (("^(.+)def test_from_hdf5_issue_731" m indent)
                (string-append indent
                               "@npt.dec.skipif(True, msg='Guix')\n"
                               m))
               ;; Unclear why this one fails.  There is no backtrace.
               (("^(.+)def test_to_dataframe_is_sparse" m indent)
                (string-append indent
                               "@npt.dec.skipif(True, msg='Guix')\n"
                               m))
               ;; These need skbio, but that neeeds biom-format.
               (("^(.+)def test_align_tree_intersect_obs" m indent)
                (string-append indent
                               "@npt.dec.skipif(True, msg='Guix')\n"
                               m))
               (("^(.+)def test_align_tree_intersect_tips" m indent)
                (string-append indent
                               "@npt.dec.skipif(True, msg='Guix')\n"
                               m))
               (("^(.+)def test_align_tree_sample" m indent)
                (string-append indent
                               "@npt.dec.skipif(True, msg='Guix')\n"
                               m))))))))
    (propagated-inputs
     (list python-anndata
           python-click
           python-flake8
           python-future
           python-h5py
           python-numpy
           python-pandas
           ;;python-scikit-bio ;mutually recursive dependency
           python-scipy))
    (native-inputs
     (list python-cython python-pytest python-pytest-cov python-nose))
    (home-page "https://www.biom-format.org")
    (synopsis "Biological Observation Matrix (BIOM) format utilities")
    (description
     "The BIOM file format is designed to be a general-use format for
representing counts of observations e.g. operational taxonomic units, KEGG
orthology groups or lipid types, in one or more biological samples
e.g. microbiome samples, genomes, metagenomes.")
    (license license:bsd-3)))

(define-public python-pairtools
  (package
    (name "python-pairtools")
    (version "1.0.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/open2c/pairtools")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-references
           (lambda _
             (substitute* '("pairtools/cli/header.py"
                            "pairtools/cli/merge.py"
                            "pairtools/cli/sort.py")
               (("/bin/bash") (which "bash")))))
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (with-directory-excursion "/tmp"
                 (invoke "pytest" "-v"))))))))
    (native-inputs
     (list python-cython python-pytest))
    (propagated-inputs
     (list htslib ; for bgzip, looked up in PATH
           samtools ; looked up in PATH
           lz4 ; for lz4c
           python-bioframe
           python-click
           python-numpy
           python-pandas
           python-pysam
           python-pyyaml
           python-scipy))
    (home-page "https://github.com/open2c/pairtools")
    (synopsis "Process mapped Hi-C data")
    (description "Pairtools is a simple and fast command-line framework to
process sequencing data from a Hi-C experiment.  Process pair-end sequence
alignments and perform the following operations:

@itemize
@item detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
  sequences of Hi-C DNA molecules
@item sort @code{.pairs} files for downstream analyses
@item detect, tag and remove PCR/optical duplicates
@item generate extensive statistics of Hi-C datasets
@item select Hi-C pairs given flexibly defined criteria
@item restore @code{.sam} alignments from Hi-C pairs.
@end itemize
")
    (license license:expat)))

(define-public python-readpaf
  (package
    (name "python-readpaf")
    (version "0.0.10")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "readpaf" version))
              (sha256
               (base32
                "15m6ffks4zwpp1ycwk6n02py6mw2yh7qr0vhpc178b91gldr97ia"))))
    (build-system pyproject-build-system)
    (arguments (list #:tests? #false))  ;there are none
    (propagated-inputs (list python-pandas))
    (home-page "https://github.com/alexomics/read-paf")
    (synopsis "Minimap2 PAF file reader")
    (description
     "This is a fast parser for minimap2 PAF (Pairwise mApping Format)
files.")
    (license license:expat)))

(define-public bioperl-minimal
  (package
    (name "bioperl-minimal")
    (version "1.7.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/bioperl/bioperl-live")
             (commit (string-append "release-"
                                    (string-map (lambda (c)
                                                  (if (char=? c #\.)
                                                      #\- c)) version)))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
    (build-system perl-build-system)
    (arguments
     (let ((transitive-inputs
            (map (compose package-name cadr)
                 (delete-duplicates
                  (concatenate
                   (map (compose package-transitive-target-inputs cadr)
                        (package-inputs this-package)))))))
       `(#:phases
         (modify-phases %standard-phases
           (add-after 'install 'wrap-programs
             (lambda* (#:key outputs #:allow-other-keys)
               ;; Make sure all executables in "bin" find the required Perl
               ;; modules at runtime.  As the PERL5LIB variable contains also
               ;; the paths of native inputs, we pick the transitive target
               ;; inputs from %build-inputs.
               (let* ((out  (assoc-ref outputs "out"))
                      (bin  (string-append out "/bin/"))
                      (path (string-join
                             (cons (string-append out "/lib/perl5/site_perl")
                                   (map (lambda (name)
                                          (assoc-ref %build-inputs name))
                                        ',transitive-inputs))
                             ":")))
                 (for-each (lambda (file)
                             (wrap-program file
                               `("PERL5LIB" ":" prefix (,path))))
                           (find-files bin "\\.pl$")))))))))
    (inputs
     (list bash-minimal perl-module-build perl-data-stag perl-libwww perl-uri))
    (native-inputs
     (list perl-test-most))
    (home-page "https://metacpan.org/release/BioPerl")
    (synopsis "Bioinformatics toolkit")
    (description
     "BioPerl is the product of a community effort to produce Perl code which
is useful in biology.  Examples include Sequence objects, Alignment objects
and database searching objects.  These objects not only do what they are
advertised to do in the documentation, but they also interact - Alignment
objects are made from the Sequence objects, Sequence objects have access to
Annotation and SeqFeature objects and databases, Blast objects can be
converted to Alignment objects, and so on.  This means that the objects
provide a coordinated and extensible framework to do computational biology.")
    (license license:perl-license)))

(define-public perl-bio-db-hts
  (package
    (name "perl-bio-db-hts")
    (version "3.01")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cpan/authors/id/A/AV/AVULLO/Bio-DB-HTS-"
                           version ".tar.gz"))
       (sha256
        (base32
         "0hjg0igfkpvh27zdkdr6pa7cqm9n6r7cwz0np74cl4wmawgvr9hj"))))
    (build-system perl-build-system)
    (native-inputs
     (list perl-module-build pkg-config))
    (propagated-inputs
     (list bioperl-minimal htslib-1.9))
    (home-page "https://metacpan.org/release/Bio-DB-HTS")
    (synopsis "Perl interface to HTS library for DNA sequencing")
    (description "This is a Perl interface to the HTS library for DNA
sequencing.")
    (license license:asl2.0)))

(define-public python-biopython
  (package
    (name "python-biopython")
    (version "1.80")
    (source (origin
              (method url-fetch)
              ;; use PyPi rather than biopython.org to ease updating
              (uri (pypi-uri "biopython" version))
              (sha256
               (base32
                "0hqf3jsxn2sphcx81fx7x3i69sarpjsi70fzw98f8rw7z2d5x02j"))))
    (build-system pyproject-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         (add-before 'check 'set-home
           ;; Some tests require a home directory to be set.
           (lambda _ (setenv "HOME" "/tmp"))))))
    (propagated-inputs
     (list python-numpy))
    (home-page "https://biopython.org/")
    (synopsis "Tools for biological computation in Python")
    (description
     "Biopython is a set of tools for biological computation including parsers
for bioinformatics files into Python data structures; interfaces to common
bioinformatics programs; a standard sequence class and tools for performing
common operations on them; code to perform data classification; code for
dealing with alignments; code making it easy to split up parallelizable tasks
into separate processes; and more.")
    (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))

(define-public python-biopython-1.73
  (package
    (inherit python-biopython)
    (version "1.73")
    (source (origin
              (method url-fetch)
              ;; use PyPi rather than biopython.org to ease updating
              (uri (pypi-uri "biopython" version))
              (sha256
               (base32
                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))))

(define-public python-fastalite
  (package
    (name "python-fastalite")
    (version "0.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "fastalite" version))
       (sha256
        (base32
         "1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj"))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #f)) ; Test data is not distributed.
    (home-page "https://github.com/nhoffman/fastalite")
    (synopsis "Simplest possible FASTA parser")
    (description "This library implements a FASTA and a FASTQ parser without
relying on a complex dependency tree.")
    (license license:expat)))

(define-public biosoup
  (package
    (name "biosoup")
    (version "0.10.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/rvaser/biosoup")
             ;; Corresponds to version 0.10.0
             (commit "38181f09854ff42cbd9632200a2ec9fb37a4b7b6")))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "02hvyka703zagx0nvv2yx3dkc748zc8g6qbrpya7r8kfkcl7y8hw"))))
    (build-system cmake-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "./bin/biosoup_test")))))))
    (native-inputs
     (list googletest))
    (home-page "https://github.com/rvaser/biosoup")
    (synopsis "C++ support library for bioinformatics tools")
    (description "Biosoup is a C++ collection of header-only data structures
used for storage and logging in bioinformatics tools.")
    (license license:expat)))

(define-public bioparser
  (package
    (name "bioparser")
    (version "3.0.13")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/rvaser/bioparser")
             ;; Corresponds to tag 3.0.13
             (commit "13341e6e0855c6b358ffcea6dad216e1009e1287")))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0c5p2dl8jb12ci9f427jzrmmm9cgvc1k4fxsn2ggkfsin6r1r82i"))))
    (build-system cmake-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "./bin/bioparser_test")))))))
    (inputs
     (list biosoup))
    (propagated-inputs
     (list zlib))
    (native-inputs
     (list googletest))
    (home-page "https://github.com/rvaser/bioparser")
    (synopsis "C++ library for parsing several formats in bioinformatics")
    (description "Bioparser is a C++ header only parsing library for several
bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib
compressed files.")
    (license license:expat)))

(define-public circtools
  (package
    (name "circtools")
    (version "1.0.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/Kevinzjy/circtools")
             ;; Corresponds to tag v1.0.0
             (commit "79380de59013601021ca3b1352d6f64d2fb89646")
             (recursive? #t)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0wg1s927g32k25j967kfr8l30nmr4c0p4zvy5igvy7cs6chd60lh"))))
    (build-system cargo-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'make-writable
           (lambda _
             (for-each make-file-writable (find-files "."))))
         (add-after 'unpack 'prepare-spoa-dependencies
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "vendor/spoa/CMakeLists.txt"
               (("find_package\\(bioparser 3.0.13 QUIET\\)")
                "find_package(bioparser 3.0.13 CONFIG)")
               (("find_package\\(biosoup 0.10.0 QUIET\\)")
                "find_package(biosoup 0.10.0 CONFIG)")
               (("GTest_FOUND") "TRUE")))))
       #:cargo-inputs
       (("rust-anyhow" ,rust-anyhow-1)
        ("rust-bio" ,rust-bio-0.33)
        ("rust-chrono" ,rust-chrono-0.4)
        ("rust-docopt" ,rust-docopt-1)
        ("rust-flate2" ,rust-flate2-1)
        ("rust-indicatif" ,rust-indicatif-0.15)
        ("rust-libc" ,rust-libc-0.2)
        ("rust-serde" ,rust-serde-1)
        ("rust-seq-io" ,rust-seq-io-0.3))))
    (inputs
     (list bioparser biosoup))
    (native-inputs
     (list cmake-minimal pkg-config googletest))
    (home-page "https://github.com/Kevinzjy/circtools")
    (synopsis "Accelerating functions in CIRI toolkit")
    (description "This package provides accelerated functions for the CIRI
toolkit.  It also provides the @code{ccs} executable to scan for circular
consensus sequences.")
    (license license:expat)))

(define-public ciri-long
  (package
    (name "ciri-long")
    (version "1.0.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/bioinfo-biols/CIRI-long")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi"))
       ;; Delete bundled binary
       (snippet '(delete-file "libs/ccs"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "setup.py"
               (("'argparse[^']*',") "") ; only for python2
               (("==") ">="))))
         (add-before 'build 'build-libssw
           (lambda _
             (with-directory-excursion "libs/striped_smith_waterman"
               (invoke "make" "libssw.so"))))
         (add-before 'build 'fix-reference-to-ccs
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "CIRI_long/pipeline.py"
               (("'ccs -i")
                (string-append "'"
                               (assoc-ref inputs "circtools") "/bin/ccs"
                               " -i")))
             ;; yuck!
             (substitute* "CIRI_long/main.py"
               (("os.chmod\\(lib_path.*") "")))))))
    (inputs
     (list circtools
           python-biopython
           python-bwapy
           python-levenshtein
           python-mappy
           python-numpy
           python-pandas
           python-pysam
           python-pyspoa
           python-scikit-learn
           python-scipy))
    (native-inputs
     (list python-cython python-nose python-setuptools))
    (home-page "https://ciri-cookbook.readthedocs.io/")
    (synopsis "Circular RNA identification for Nanopore sequencing")
    (description "CIRI-long is a package for circular RNA identification using
long-read sequencing data.")
    (license license:expat)))

(define-public qtltools
  (package
    (name "qtltools")
    (version "1.3.1")
    (source (origin
              (method url-fetch/tarbomb)
              (uri (string-append "https://qtltools.github.io/qtltools/"
                                  "binaries/QTLtools_" version
                                  "_source.tar.gz"))
              (sha256
               (base32
                "13gdry5l43abn3464fmk8qzrxgxnxah2612r66p9dzhhl92j30cd"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; no tests included
       #:make-flags
       ,#~(list (string-append "BOOST_INC="
                               #$(this-package-input "boost") "/include")
                (string-append "BOOST_LIB="
                               #$(this-package-input "boost") "/lib")
                (string-append "HTSLD_INC="
                               #$(this-package-input "htslib") "/include")
                (string-append "HTSLD_LIB="
                               #$(this-package-input "htslib") "/lib")
                (string-append "RMATH_INC="
                               #$(this-package-input "rmath-standalone")
                               "/include")
                (string-append "RMATH_LIB="
                               #$(this-package-input "rmath-standalone")
                               "/lib"))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-linkage
           (lambda _
             (substitute* "qtltools/Makefile"
               (("libboost_iostreams.a")
                "libboost_iostreams.so")
               (("libboost_program_options.a")
                "libboost_program_options.so")
               (("-lblas") "-lopenblas"))))
         (add-before 'build 'chdir
           (lambda _ (chdir "qtltools")))
         (replace 'configure
           (lambda _
             (substitute* "qtltools/Makefile"
               (("LIB_FLAGS=-lz")
                "LIB_FLAGS=-lz -lcrypto -lssl")
               (("LIB_FILES=\\$\\(RMATH_LIB\\)/libRmath.a \
\\$\\(HTSLD_LIB\\)/libhts.a \
\\$\\(BOOST_LIB\\)/libboost_iostreams.a \
\\$\\(BOOST_LIB\\)/libboost_program_options.a")
                "LIB_FILES=$(RMATH_LIB)/libRmath.so \
$(HTSLD_LIB)/libhts.so \
$(BOOST_LIB)/libboost_iostreams.so \
$(BOOST_LIB)/libboost_program_options.so"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (mkdir-p bin)
               (install-file "bin/QTLtools" bin)))))))
    (inputs
     (list curl
           gsl
           boost
           rmath-standalone
           htslib-1.3
           openssl
           openblas
           zlib))
    (home-page "https://qtltools.github.io/qtltools/")
    (synopsis "Tool set for molecular QTL discovery and analysis")
    (description "QTLtools is a tool set for molecular QTL discovery
and analysis.  It allows going from the raw genetic sequence data to
collection of molecular @dfn{Quantitative Trait Loci} (QTLs) in few
easy-to-perform steps.")
    (license license:gpl3+)))

(define-public bpp-core
  (package
    (name "bpp-core")
    (version "2.4.1")
    (source
      (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/BioPP/bpp-core")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"))))
    (build-system cmake-build-system)
    ;; XXX: does not build with later GCC:
    ;; error: ‘numeric_limits’ was not declared in this scope
    (native-inputs (list gcc-10))
    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-core/html/index.html")
    (synopsis "C++ libraries for Bioinformatics")
    (description
     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.  It is
Object Oriented and is designed to be both easy to use and computer efficient.
Bio++ intends to help programmers to write computer expensive programs, by
providing them a set of re-usable tools.")
      (license license:cecill-c)))

(define-public bpp-phyl
  (package
    (name "bpp-phyl")
    (version "2.4.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BioPP/bpp-phyl")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"))))
    (build-system cmake-build-system)
    (inputs
     (list bpp-core bpp-seq))
    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/")
    (synopsis "Bio++ phylogenetic library")
    (description
     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.  This
library provides phylogenetics-related modules.")
    (license license:cecill-c)))

(define-public bpp-phyl-omics
  (package
    (name "bpp-phyl-omics")
    (version "2.4.1")
    (source
      (origin
       (method git-fetch)
       (uri (git-reference
            (url "https://github.com/BioPP/bpp-phyl-omics")
            (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32 "172psb8njkjwg3cd6gdy5w0mq8f0817v635yw4bk7146aggjzl1h"))))
    (build-system cmake-build-system)
    (arguments
     (list #:tests? #f)) ; No test provided.
    (inputs
     (list bpp-core
           bpp-phyl
           bpp-seq
           bpp-seq-omics))
    (home-page "https://github.com/BioPP/bpp-phyl-omics")
    (synopsis "Bio++ phylogenetic library genomics components")
    (description
     "This library contains the genomics components of the Bio++ phylogenetics
library.  It is part of the Bio++ project.")
    (license license:cecill)))

(define-public bpp-popgen
  (package
    (name "bpp-popgen")
    (version "2.4.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BioPP/bpp-popgen")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"))))
    (build-system cmake-build-system)
    (arguments
     (list #:tests? #f)) ; There are no tests.
    (inputs
     (list bpp-core bpp-seq))
    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/")
    (synopsis "Bio++ population genetics library")
    (description
     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.  This
library provides population genetics-related modules.")
    (license license:cecill-c)))

(define-public bpp-seq
  (package
    (name "bpp-seq")
    (version "2.4.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BioPP/bpp-seq")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32 "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"))))
    (build-system cmake-build-system)
    (inputs
     (list bpp-core))
    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/")
    (synopsis "Bio++ sequence library")
    (description
     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.  This
library provides sequence-related modules.")
    (license license:cecill-c)))

(define-public bpp-seq-omics
  (package
    (name "bpp-seq-omics")
    (version "2.4.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BioPP/bpp-seq-omics")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32 "1sc2xdfnfp5a6qihplp49rgrqmj89898avfy9bqaq1g2fajppgjj"))))
    (build-system cmake-build-system)
    (inputs
     (list bpp-core bpp-seq))
    (home-page "https://github.com/BioPP/bpp-seq-omics")
    (synopsis "Bio++ sequence library genomics components")
    (description
     "This library contains the genomics components of the Bio++ sequence library.
It is part of the Bio++ project.")
    (license license:cecill)))

(define-public bppsuite
  (package
    (name "bppsuite")
    (version "2.4.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BioPP/bppsuite")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"))))
    (build-system cmake-build-system)
    (arguments
     (list #:tests? #f)) ; There are no tests.
    (native-inputs
     (list groff man-db texinfo))
    (inputs
     (list bpp-core bpp-seq bpp-phyl bpp-popgen))
    (home-page "https://github.com/BioPP")
    (synopsis "Bioinformatics tools written with the Bio++ libraries")
    (description
     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.  This
package provides command line tools using the Bio++ library.")
    (license license:cecill-c)))

(define-public blast+
  (package
    (name "blast+")
    (version "2.14.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
                    version "/ncbi-blast-" version "+-src.tar.gz"))
              (sha256
               (base32
                "003mn7m4y306k7visv3in3ikfgm8m41z0jq9lyvz10iv1hdpyixz"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Remove bundled bzip2, zlib and pcre.
                  (delete-file-recursively "c++/src/util/compress/bzip2")
                  (delete-file-recursively "c++/src/util/compress/zlib")
                  (delete-file-recursively "c++/src/util/regexp")
                  (substitute* "c++/src/util/compress/Makefile.in"
                    (("bzip2 zlib api") "api"))
                  ;; Remove useless msbuild directory
                  (delete-file-recursively
                   "c++/src/build-system/project_tree_builder/msbuild")

                  ;; Build reproducibly.
                  ;; Do not record the kernel version
                  (substitute* "c++/src/build-system/configure"
                    (("kver=.*") "kver=\"\""))
                  ;; Do not generate random numbers.
                  (substitute* "c++/scripts/common/impl/define_random_macros.sh"
                    (("#define NCBI_RANDOM_VALUE_MAX  0xffffffffu" m)
                     (string-append m "
#define NCBI_RANDOM_VALUE_0    2845495105u
#define NCBI_RANDOM_VALUE_1    2158634051u
#define NCBI_RANDOM_VALUE_2    4072202242u
#define NCBI_RANDOM_VALUE_3    902228395u
#define NCBI_RANDOM_VALUE_4    1353323915u
#define NCBI_RANDOM_VALUE_5    574823513u
#define NCBI_RANDOM_VALUE_6    4119501261u
#define NCBI_RANDOM_VALUE_7    2477640938u
#define NCBI_RANDOM_VALUE_8    2776595395u
#define NCBI_RANDOM_VALUE_9    270550684u
"))
                    (("cksum") "cksum >/dev/null"))))))
    (build-system gnu-build-system)
    (arguments
     (list
      ;; There are two(!) tests for this massive library, and both fail with
      ;; "unparsable timing stats".
      ;; ERR [127] --  [serial/datatool] datatool.sh     (unparsable timing stats)
      ;; ERR [127] --  [serial/datatool] datatool_xml.sh     (unparsable timing stats)
      #:tests? #f
      #:out-of-source? #t
      #:parallel-build? #f              ;not supported
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'configure 'set-HOME
            ;; $HOME needs to be set at some point during the configure phase
            (lambda _ (setenv "HOME" "/tmp")))
          (add-after 'unpack 'enter-dir
            (lambda _ (chdir "c++")))
          (add-after 'enter-dir 'fix-build-system
            (lambda _
              (define (which* cmd)
                (cond ((string=? cmd "date")
                       ;; make call to "date" deterministic
                       "date -d @0")
                      ((which cmd)
                       => identity)
                      (else
                       (format (current-error-port)
                               "WARNING: Unable to find absolute path for ~s~%"
                               cmd)
                       #false)))

              ;; Rewrite hardcoded paths to various tools
              (substitute* (append '("src/build-system/configure.ac"
                                     "src/build-system/configure"
                                     "src/build-system/helpers/run_with_lock.c"
                                     "scripts/common/impl/if_diff.sh"
                                     "scripts/common/impl/run_with_lock.sh"
                                     "src/build-system/Makefile.configurables.real"
                                     "src/build-system/Makefile.in.top"
                                     "src/build-system/Makefile.meta.gmake=no"
                                     "src/build-system/Makefile.meta.in"
                                     "src/build-system/Makefile.meta_l"
                                     "src/build-system/Makefile.meta_p"
                                     "src/build-system/Makefile.meta_r"
                                     "src/build-system/Makefile.mk.in"
                                     "src/build-system/Makefile.requirements"
                                     "src/build-system/Makefile.rules_with_autodep.in")
                                   (find-files "scripts/common/check" "\\.sh$"))
                (("(/usr/bin/|/bin/)([a-z][-_.a-z]*(\\+\\+)?)" all dir cmd)
                 (or (which* cmd) all)))

              (substitute* (find-files "src/build-system" "^config.*")
                (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
                (("^PATH=.*") ""))

              ;; rewrite "/var/tmp" in check script
              (substitute* "scripts/common/check/check_make_unix.sh"
                (("/var/tmp") "/tmp"))

              ;; do not reset PATH
              (substitute* (find-files "scripts/common/impl/" "\\.sh$")
                (("^ *PATH=.*") "")
                (("action=/bin/") "action=")
                (("export PATH") ":"))))
          (replace 'configure
            (lambda _
              (let ((lib     (string-append #$output:lib "/lib"))
                    (include (string-append #$output:include
                                            "/include/ncbi-tools++")))
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
                (invoke "./configure.orig"
                        (string-append "--with-build-root=" (getcwd) "/build")
                        (string-append "--prefix=" #$output)
                        (string-append "--libdir=" lib)
                        (string-append "--includedir=" include)
                        (string-append "--with-bz2="
                                       #$(this-package-input "bzip2"))
                        (string-append "--with-z="
                                       #$(this-package-input "zlib"))
                        (string-append "--with-pcre="
                                       #$(this-package-input "pcre"))
                        ;; Each library is built twice by default, once
                        ;; with "-static" in its name, and again
                        ;; without.
                        "--without-static"
                        "--with-dll")))))))
    (outputs '("out"       ;  21 MB
               "lib"       ; 226 MB
               "include")) ;  33 MB
    (inputs
     (list bzip2
           lmdb
           zlib
           pcre
           perl
           python-wrapper))
    (native-inputs
     (list cpio))
    (home-page "https://blast.ncbi.nlm.nih.gov")
    (synopsis "Basic local alignment search tool")
    (description
     "BLAST is a popular method of performing a DNA or protein sequence
similarity search, using heuristics to produce results quickly.  It also
calculates an “expect value” that estimates how many matches would have
occurred at a given score by chance, which can aid a user in judging how much
confidence to have in an alignment.")
    ;; Most of the sources are in the public domain, with the following
    ;; exceptions:
    ;;   * Expat:
    ;;     * ./c++/include/util/bitset/
    ;;     * ./c++/src/html/ncbi_menu*.js
    ;;   * Boost license:
    ;;     * ./c++/include/util/impl/floating_point_comparison.hpp
    ;;   * LGPL 2+:
    ;;     * ./c++/include/dbapi/driver/odbc/unix_odbc/
    ;;   * ASL 2.0:
    ;;     * ./c++/src/corelib/teamcity_*
    (license (list license:public-domain
                   license:expat
                   license:boost1.0
                   license:lgpl2.0+
                   license:asl2.0))))

(define-public bless
  (package
    (name "bless")
    (version "1p02")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
                                  version ".tgz"))
              (sha256
               (base32
                "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
              (modules '((guix build utils)))
              (snippet
               `(begin
                  ;; Remove bundled boost, pigz, zlib, and .git directory
                  ;; FIXME: also remove bundled sources for murmurhash3 and
                  ;; kmc once packaged.
                  (delete-file-recursively "boost")
                  (delete-file-recursively "pigz")
                  (delete-file-recursively "google-sparsehash")
                  (delete-file-recursively "zlib")
                  (delete-file-recursively ".git")))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:make-flags
       ,#~(list (string-append "ZLIB="
                               #$(this-package-input "zlib")
                               "/lib/libz.so")
                (string-append "LDFLAGS="
                               (string-join '("-lboost_filesystem"
                                              "-lboost_system"
                                              "-lboost_iostreams"
                                              "-lz"
                                              "-fopenmp"))))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'do-not-build-bundled-pigz
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (substitute* "Makefile"
              (("cd pigz/pigz-2.3.3; make") ""))))
         (add-after 'unpack 'patch-paths-to-executables
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (substitute* "parse_args.cpp"
              (("kmc_binary = .*")
               (string-append "kmc_binary = \""
                              (assoc-ref outputs "out")
                              "/bin/kmc\";"))
              (("pigz_binary = .*")
               (string-append "pigz_binary = \""
                              (assoc-ref inputs "pigz")
                              "/bin/pigz\";")))))
         (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
              (for-each (lambda (file)
                          (install-file file bin))
                        '("bless" "kmc/bin/kmc")))))
         (delete 'configure))))
    (native-inputs
     (list perl))
    (inputs
     (list openmpi boost sparsehash pigz zlib))
    (supported-systems '("x86_64-linux"))
    (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
    (synopsis "Bloom-filter-based error correction tool for NGS reads")
    (description
     "@dfn{Bloom-filter-based error correction solution for high-throughput
sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
correction tool for genomic reads produced by @dfn{Next-generation
sequencing} (NGS).  BLESS produces accurate correction results with much less
memory compared with previous solutions and is also able to tolerate a higher
false-positive rate.  BLESS can extend reads like DNA assemblers to correct
errors at the end of reads.")
    (license license:gpl3+)))

(define-public bowtie
  (package
    (name "bowtie")
    (version "2.3.4.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BenLangmead/bowtie2")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (substitute* "Makefile"
                    ;; replace BUILD_HOST and BUILD_TIME for deterministic build
                    (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
                    (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       ,#~(list "allall"
                "WITH_TBB=1"
                (string-append "prefix=" #$output))
       #:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda _
             ;; This "extended character" is not considered valid.
             (substitute* "processor_support.h"
               (("“") "\"")
               (("”") "\""))))
         (replace 'check
           (lambda _
             (invoke "perl"
                     "scripts/test/simple_tests.pl"
                     "--bowtie2=./bowtie2"
                     "--bowtie2-build=./bowtie2-build"))))))
    (inputs
     `(("tbb" ,tbb-2020)
       ("zlib" ,zlib)
       ("python" ,python-wrapper)))
    (native-inputs
     (list perl perl-clone perl-test-deep perl-test-simple))
    (home-page "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
    (synopsis "Fast and sensitive nucleotide sequence read aligner")
    (description
     "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
reads to long reference sequences.  It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good at
aligning to relatively long (e.g. mammalian) genomes.  Bowtie 2 indexes the
genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB.  Bowtie 2 supports
gapped, local, and paired-end alignment modes.")
    (supported-systems '("x86_64-linux"))
    (license license:gpl3+)))

(define-public bowtie1
  (package
    (name "bowtie1")
    (version "1.3.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
                                  version "/bowtie-" version "-src.zip"))
              (sha256
               (base32
                "0q87nhgj9wrnbazcpvqp4594hmyh1isi3s9b2wlghvl4afm1fdg2"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "Makefile"
                  ;; replace BUILD_HOST and BUILD_TIME for deterministic build
                  (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; Tests need various perl modules
       #:test-target "simple-test"
       #:make-flags
       ,#~(append #$(if (not (target-x86?))
                        #~'("POPCNT_CAPABILITY=0")
                        #~'())
                  (list (string-append "CC=" #$(cc-for-target))
                        (string-append "CXX=" #$(cxx-for-target))
                        "all"
                        (string-append "prefix=" #$output)))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (inputs
     (list python-wrapper tbb zlib))
    (supported-systems %64bit-supported-systems)
    (home-page "https://bowtie-bio.sourceforge.net/index.shtml")
    (synopsis "Fast aligner for short nucleotide sequence reads")
    (description
     "Bowtie is a fast, memory-efficient short read aligner.  It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.  Bowtie indexes the genome with a Burrows-Wheeler index to
keep its memory footprint small: typically about 2.2 GB for the human
genome (2.9 GB for paired-end).")
    (license license:artistic2.0)))

(define-public tophat
  (package
    (name "tophat")
    (version "2.1.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
                    version ".tar.gz"))
              (sha256
               (base32
                "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Remove bundled SeqAn and samtools
                  (delete-file-recursively "src/SeqAn-1.4.2")
                  (delete-file-recursively "src/samtools-0.1.18")))))
    (build-system gnu-build-system)
    (arguments
     '(#:parallel-build? #f             ; not supported
       #:phases
       (modify-phases %standard-phases
         (add-after 'set-paths 'hide-default-gcc
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((gcc (assoc-ref inputs "gcc")))
               ;; Remove the default GCC from CPLUS_INCLUDE_PATH to prevent
               ;; conflicts with the GCC 5 input.
               (setenv "CPLUS_INCLUDE_PATH"
                       (string-join
                        (delete (string-append gcc "/include/c++")
                                (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
                        ":")))))
         (add-after 'unpack 'use-system-samtools
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "src/Makefile.in"
               (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
               (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
               (("SAMPROG = samtools_0\\.1\\.18") "")
               (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
               (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
             (substitute* '("src/common.cpp"
                            "src/tophat.py")
               (("samtools_0.1.18") (which "samtools")))
             (substitute* '("src/common.h"
                            "src/bam2fastx.cpp")
               (("#include \"bam.h\"") "#include <samtools/bam.h>")
               (("#include \"sam.h\"") "#include <samtools/sam.h>"))
             (substitute* '("src/bwt_map.h"
                            "src/map2gtf.h"
                            "src/align_status.h")
               (("#include <bam.h>") "#include <samtools/bam.h>")
               (("#include <sam.h>") "#include <samtools/sam.h>")))))))
    (native-inputs
     `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions
    (inputs
     `(("boost" ,boost)
       ("bowtie" ,bowtie)
       ("ncurses" ,ncurses)
       ("perl" ,perl)
       ("python" ,python-2)
       ("samtools" ,samtools-0.1)
       ("seqan" ,seqan-1)
       ("zlib" ,zlib)))
    (home-page "https://ccb.jhu.edu/software/tophat/index.shtml")
    (synopsis "Spliced read mapper for RNA-Seq data")
    (description
     "TopHat is a fast splice junction mapper for nucleotide sequence
reads produced by the RNA-Seq method.  It aligns RNA-Seq reads to
mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify
splice junctions between exons.")
    ;; TopHat is released under the Boost Software License, Version 1.0
    ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
    (license license:boost1.0)))

(define-public bwa
  (package
    (name "bwa")
    (version "0.7.18")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/lh3/bwa")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1vf3iwkzxqkzhcfz2q3qyvcv3jrvbb012qy21pfgjl8lv20ywfr1"))))
    (build-system gnu-build-system)
    (arguments
     (list #:tests? #f ;no "check" target
           #:make-flags #~(list "CFLAGS=-fcommon"
                                (string-append "CC=" #$(cc-for-target)))
           #:phases
           #~(modify-phases %standard-phases
               (replace 'install
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let* ((out (assoc-ref outputs "out"))
                          (bin (string-append out "/bin"))
                          (lib (string-append out "/lib"))
                          (doc (string-append out "/share/doc/bwa"))
                          (man (string-append out "/share/man/man1")))
                     (install-file "bwa" bin)
                     (install-file "libbwa.a" lib)
                     (install-file "README.md" doc)
                     (install-file "bwa.1" man))))
               ;; no "configure" script
               (delete 'configure))))
    (inputs (list zlib))
    (supported-systems '("x86_64-linux" "aarch64-linux"))
    (home-page "https://bio-bwa.sourceforge.net/")
    (synopsis "Burrows-Wheeler sequence aligner")
    (description
     "BWA is a software package for mapping low-divergent sequences against a
large reference genome, such as the human genome.  It consists of three
algorithms: BWA-backtrack, BWA-SW and BWA-MEM.  The first algorithm is
designed for Illumina sequence reads up to 100bp, while the rest two for
longer sequences ranged from 70bp to 1Mbp.  BWA-MEM and BWA-SW share similar
features such as long-read support and split alignment, but BWA-MEM, which is
the latest, is generally recommended for high-quality queries as it is faster
and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
    (license license:gpl3+)))

(define-public bwa-pssm
  (package
    (inherit bwa)
    (name "bwa-pssm")
    (version "0.5.11")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/pkerpedjiev/bwa-pssm")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r"))))
    (build-system gnu-build-system)
    (arguments
     (substitute-keyword-arguments (package-arguments bwa)
       ((#:phases phases #~%standard-phases)
        #~(modify-phases #$phases
            (add-after 'unpack 'patch-C-error
              (lambda _
                (substitute* "pssm.c"
                  (("inline int map") "int map"))))))))
    (inputs
     (list gdsl zlib perl))
    ;; https://bwa-pssm.binf.ku.dk is down, and all Web Archived copies are
    ;; blank (they actually have "display:none" for some nefarious reason).
    (home-page "https://github.com/pkerpedjiev/bwa-pssm")
    (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
    (description
     "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
the use of @dfn{position specific scoring matrices} (PSSM).  Like many of the
existing aligners it is fast and sensitive.  Unlike most other aligners,
however, it is also adaptible in the sense that one can direct the alignment
based on known biases within the data set.  It is coded as a modification of
the original BWA alignment program and shares the genome index structure as
well as many of the command line options.")
    (license license:gpl3+)))

(define-public bwa-meth
  (package
    (name "bwa-meth")
    (version "0.2.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/brentp/bwa-meth")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0c695lkrr0996zwkibl7324wg2vxmn6522sz30xv4a9gaf0lnbh3"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'keep-references-to-bwa
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "bwameth.py"
               (("bwa (mem|index)" _ command)
                (string-append (which "bwa") " " command))
               ;; There's an ill-advised check for "samtools" on PATH.
               (("^checkX.*") "")))))))
    (inputs
     (list bwa))
    (native-inputs
     (list python-toolshed))
    (home-page "https://github.com/brentp/bwa-meth")
    (synopsis "Fast and accurante alignment of BS-Seq reads")
    (description
     "BWA-Meth works for single-end reads and for paired-end reads from the
directional protocol (most common).  It uses the method employed by
methylcoder and Bismark of in silico conversion of all C's to T's in both
reference and reads.  It recovers the original read (needed to tabulate
methylation) by attaching it as a comment which BWA appends as a tag to the
read.  It performs favorably to existing aligners gauged by number of on and
off-target reads for a capture method that targets CpG-rich region.")
    (license license:expat)))

(define-public python-bx-python
  (package
    (name "python-bx-python")
    (version "0.9.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/bxlab/bx-python")
                    (commit "4f4a48d3f227ae390c1b22072867ba86e347bdef")))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1c914rw8phiw7zwzngz9i9hdciz5lq53drwdbpl2bd2sf5bj2biy"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-before 'check 'build-extensions
           (lambda _
             ;; Cython extensions have to be built before running the tests.
             (invoke "python" "setup.py" "build_ext" "--inplace")))
         ;; Unrecognized argument.
         (add-after 'unpack 'disable-cython-doctests
           (lambda _ (substitute* "pytest.ini" (("--doctest-cython") "")))))))
    (propagated-inputs
     (list python-numpy))
    (inputs
     (list zlib))
    (native-inputs
     (list python-cython python-lzo python-pytest))
    (home-page "https://github.com/bxlab/bx-python")
    (synopsis "Tools for manipulating biological data")
    (description
     "bx-python provides tools for manipulating biological data, particularly
multiple sequence alignments.")
    (license license:expat)))

(define-public python-mofax
  ;; This is a recent commit from the "dev" branch, which is much more recent
  ;; than the latest commit from the "master" branch.
  (let ((commit "4d96f8f0a5d5251847353656f523684d66c3c47a")
        (revision "0"))
    (package
      (name "python-mofax")
      (version (git-version "0.4.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/bioFAM/mofax")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1lwrw0qyvvnyiqz1l20dhcf7dxidb80cqgvk78czvdgba87yxzqx"))
                (modules '((guix build utils)))
                ;; Prevent the pyproject-build-system from guessing that flit
                ;; should be used as a builder.
                (snippet '(substitute* "pyproject.toml"
                            (("^#.*") "")))))
      (build-system pyproject-build-system)
      (arguments
       (list
        ;; This test is failing due to a bug. The bug has been reported to the
        ;; developers. See https://github.com/bioFAM/mofax/issues/12 for more
        ;; info.
        #:test-flags '(list "-k" "not test_get_methods")))
      (propagated-inputs (list python-h5py
                               python-matplotlib
                               python-pandas
                               python-poetry-core
                               python-scipy
                               python-seaborn))
      (native-inputs (list python-numpy python-pytest))
      (home-page "https://github.com/bioFAM/mofax")
      (synopsis
       "Motif activity finder for transcription factor motif analysis")
      (description
       "MoFax is a Python package for transcription factor motif analysis.
It provides convenience functions to load and visualize factor models trained
with MOFA+ in Python.")
      (license license:expat))))

(define-public python-mudata
  (package
    (name "python-mudata")
    (version "0.2.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/scverse/mudata")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "02h0k1q57589r0hdv8nwg1vk7g2ljvn5g66c47fy5gdilbm3gjws"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-anndata python-h5py python-pandas))
    (native-inputs
     (list python-flit-core python-numpy python-pytest python-zarr))
    (home-page "https://github.com/scverse/mudata")
    (synopsis "Python package for multi-omics data analysis")
    (description
     "Mudata is a Python package for multi-omics data analysis.
It is designed to provide functionality to load, process, and store multimodal
omics data.")
    (license license:bsd-3)))

(define-public python-mofapy2
  (package
    (name "python-mofapy2")
    (version "0.7.1")
    (source
     (origin
       ;; The tarball from PyPi doesn't include tests.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/bioFAM/mofapy2")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0ahhnqk6gjrhyq286mrd5n7mxcv8l6040ffsawbjx9maqx8wbam0"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; cupy is an optional dependency, which
      ;; itself has nonfree dependencies (CUDA)
      '(list "--ignore=mofapy2/notebooks/test_cupy.py")))
    (propagated-inputs (list python-anndata
                             python-h5py
                             python-numpy
                             python-pandas
                             python-scikit-learn
                             python-scipy))
    (native-inputs (list python-poetry-core
                         python-pytest))
    (home-page "https://biofam.github.io/MOFA2/")
    (synopsis "Multi-omics factor analysis")
    (description "MOFA is a factor analysis model that provides a general
framework for the integration of multi-omic data sets in an unsupervised
fashion.  Intuitively, MOFA can be viewed as a versatile and statistically
rigorous generalization of principal component analysis to multi-omics data.
Given several data matrices with measurements of multiple -omics data types on
the same or on overlapping sets of samples, MOFA infers an interpretable
low-dimensional representation in terms of a few latent factors.  These learnt
factors represent the driving sources of variation across data modalities,
thus facilitating the identification of cellular states or disease
subgroups.")
    (license license:lgpl3)))

(define-public python-muon
  (package
    (name "python-muon")
    (version "0.1.6")
    (source
     (origin
       ;; The tarball from PyPi doesn't include tests.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/scverse/muon")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1kd3flgy41dc0sc71wfnirh8vk1psxgyjxkbx1zx9yskkh6anbgw"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; Even providing a random seed, scipy.sparse.rand produces inconsistent
      ;; results across scipy versions.
      '(list "-k" "not test_tfidf")
      #:phases
      '(modify-phases %standard-phases
         ;; Numba needs a writable dir to cache functions.
         (add-before 'build 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs (list python-anndata
                             python-h5py
                             python-matplotlib
                             python-mofapy2
                             python-mudata
                             python-numba
                             python-numpy
                             python-pandas
                             python-protobuf
                             python-pybedtools
                             python-pysam
                             python-scanpy
                             python-scikit-learn
                             python-seaborn
                             python-tqdm
                             python-umap-learn))
    (native-inputs (list python-flit-core
                         python-pytest
                         python-pytest-flake8))
    (home-page "https://github.com/scverse/muon")
    (synopsis "Multimodal omics analysis framework")
    (description "muon is a multimodal omics Python framework.")
    (license license:bsd-3)))

(define-public python-pyega3
  (deprecated-package "python-pyega3" python-ega-download-client))

(define-public python-pysam
  (package
    (name "python-pysam")
    (version "0.20.0")
    (source (origin
              (method git-fetch)
              ;; Test data is missing on PyPi.
              (uri (git-reference
                    (url "https://github.com/pysam-developers/pysam")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1dq6jwwm98lm30ijdgqc5xz5ppda4nj999y6qs78mhw8x0kij8gg"))
              (modules '((guix build utils)))
              (snippet '(begin
                          ;; FIXME: Unbundle samtools and bcftools.
                          (delete-file-recursively "htslib")))))
    (build-system pyproject-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'set-flags
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "HTSLIB_MODE" "external")
             (setenv "HTSLIB_LIBRARY_DIR"
                     (string-append (assoc-ref inputs "htslib") "/lib"))
             (setenv "HTSLIB_INCLUDE_DIR"
                     (string-append (assoc-ref inputs "htslib") "/include"))
             (setenv "LDFLAGS" "-lncurses")
             (setenv "CFLAGS" "-D_CURSES_LIB=1")))
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               ;; Step out of source dir so python does not import from CWD.
               (with-directory-excursion "tests"
                 (setenv "HOME" "/tmp")
                 (invoke "make" "-C" "pysam_data")
                 (invoke "make" "-C" "cbcf_data")
                 ;; The FileHTTP test requires network access.
                 (invoke "pytest" "-k" "not FileHTTP"))))))))
    (propagated-inputs
     (list htslib))                    ; Included from installed header files.
    (inputs
     (list ncurses curl zlib))
    (native-inputs
     (list python-cython
           python-pytest
           ;; Dependencies below are are for tests only.
           samtools
           bcftools))
    (home-page "https://github.com/pysam-developers/pysam")
    (synopsis "Python bindings to the SAMtools C API")
    (description
     "Pysam is a Python module for reading and manipulating files in the
SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
also includes an interface for tabix.")
    (license license:expat)))

(define-public python-twobitreader
  (package
    (name "python-twobitreader")
    (version "3.1.6")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/benjschiller/twobitreader")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62"))))
    (build-system python-build-system)
    ;; Tests are not included
    (arguments '(#:tests? #f))
    (native-inputs
     (list python-sphinx))
    (home-page "https://github.com/benjschiller/twobitreader")
    (synopsis "Python library for reading .2bit files")
    (description
     "twobitreader is a Python library for reading .2bit files as used by the
UCSC genome browser.")
    (license license:artistic2.0)))

(define-public python-plastid
  (package
    (name "python-plastid")
    (version "0.6.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/joshuagryphon/plastid")
                    (commit "d97f239d73b3a7c2eff46f71928b777431891f90")))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0iccpywlpf1ws46279z9rl0l29pil0rj0g2j5nvqq7jfbnq581cf"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "plastid/test"
             ;; These four failures look like errors in the test wrapper
             ;; class.
             "-k" (string-append "not test_chrom_sizes"
                                 " and not test_no_crash_if_file_not_exist"
                                 " and not test_fiveprime_variable"
                                 " and not test_fiveprime_variable_from_file"))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'unpack-test-data
            (lambda* (#:key inputs #:allow-other-keys)
              (invoke "tar" "-C" "plastid/test"
                      "-xf" (assoc-ref inputs "test-data"))
              ;; This one requires bowtie-build
              (delete-file "plastid/test/functional/test_crossmap.py")))
          (add-after 'unpack 'patch-for-python-3.10
            (lambda _
              ;; Some classes were moved from collections to collections.abc
              ;; in Python 3.10.
              (substitute* "plastid/readers/bigbed.pyx"
                ((", Iterable")
                 "\nfrom collections.abc import Iterable"))))
          (add-before 'check 'build-extensions
            (lambda _
              ;; Cython extensions have to be built before running the tests.
              (invoke "python3" "setup.py" "build_ext" "--inplace"))))))
    (propagated-inputs
     (list python-numpy
           python-scipy
           python-pandas
           python-pysam
           python-matplotlib
           python-biopython
           python-twobitreader
           python-termcolor))
    (inputs
     (list openssl))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-pytest" ,python-pytest)
       ("test-data"
        ,(origin
           (method url-fetch)
           (uri "https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=1")
           (file-name "plastid-test-data-2022-05-04.tar.bz2")
           (sha256
            (base32 "1szsji06m2r21flnvxg84jnj5zmlk6z10c9651v9ag71nxj9rbzn"))))))
    (home-page "https://github.com/joshuagryphon/plastid")
    (synopsis "Python library for genomic analysis")
    (description
     "plastid is a Python library for genomic analysis – in particular,
high-throughput sequencing data – with an emphasis on simplicity.")
    (license license:bsd-3)))

(define-public tetoolkit
  (package
    (name "tetoolkit")
    (version "2.2.1b")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/mhammell-laboratory/TEtranscripts")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'adjust-requirements
           (lambda _
             (substitute* "setup.py"
               ;; This defunct dependency isn't required for Python 3 (see:
               ;; https://github.com/mhammell-laboratory/TEtranscripts/issues/111).
               ((".*'argparse'.*") ""))))
         (add-after 'unpack 'patch-invocations
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* '("bin/TEtranscripts"
                            "bin/TEcount")
               (("'sort ")
                (string-append "'" (search-input-file inputs "bin/sort") " "))
               (("'rm -f ")
                (string-append "'" (search-input-file inputs "bin/rm") " -f "))
               (("'Rscript'")
                (string-append "'" (search-input-file inputs "bin/Rscript")
                               "'")))
             (substitute* "TEToolkit/IO/ReadInputs.py"
               (("BamToBED")
                (search-input-file inputs "bin/bamToBed")))
             (substitute* "TEToolkit/Normalization.py"
               (("\"Rscript\"")
                (string-append "\"" (search-input-file inputs "bin/Rscript")
                               "\"")))))
         (add-after 'install 'wrap-program
           (lambda* (#:key outputs #:allow-other-keys)
             ;; Make sure the executables find R packages.
             (for-each (lambda (script)
                         (wrap-program script
                           `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
                       (list (search-input-file outputs "bin/TEtranscripts")
                             (search-input-file outputs "bin/TEcount"))))))))
    (inputs
     (list bash-minimal
           coreutils
           bedtools
           python-pysam
           r-minimal
           r-deseq2))
    (home-page "https://github.com/mhammell-laboratory/TEtranscripts")
    (synopsis "Transposable elements in differential enrichment analysis")
    (description
     "This is package for including transposable elements in differential
enrichment analysis of sequencing datasets.  TEtranscripts and TEcount take
RNA-seq (and similar data) and annotates reads to both genes and transposable
elements.  TEtranscripts then performs differential analysis using DESeq2.
Note that TEtranscripts and TEcount rely on specially curated GTF files, which
are not included due to their size.")
    (license license:gpl3+)))

(define-public cd-hit
  (package
    (name "cd-hit")
    (version "4.8.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/weizhongli/cdhit"
                                  "/releases/download/V" version
                                  "/cd-hit-v" version
                                  "-2019-0228.tar.gz"))
              (sha256
               (base32
                "1phmfhgcpyfd6kj7jwzw976613lcpv1wc2pzfdfaxla062x2s5r6"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ; there are no tests
      #:make-flags
      ;; Executables are copied directly to the PREFIX.
      #~(list (string-append "PREFIX=" #$output "/bin")
              ;; Support longer sequences (e.g. Pacbio sequences)
              "MAX_SEQ=60000000")
      #:phases
      '(modify-phases %standard-phases
         ;; No "configure" script
         (delete 'configure)
         ;; Remove sources of non-determinism
         (add-after 'unpack 'be-timeless
           (lambda _
             (substitute* "cdhit-utility.c++"
               ((" \\(built on \" __DATE__ \"\\)") ""))
             (substitute* "cdhit-common.c++"
               (("__DATE__") "\"0\"")
               (("\", %s, \" __TIME__ \"\\\\n\", date") ""))))
         ;; The "install" target does not create the target directory.
         (add-before 'install 'create-target-dir
           (lambda* (#:key outputs #:allow-other-keys)
             (mkdir-p (string-append (assoc-ref outputs "out") "/bin")))))))
    (inputs
     (list perl zlib))
    (home-page "http://weizhongli-lab.org/cd-hit/")
    (synopsis "Cluster and compare protein or nucleotide sequences")
    (description
     "CD-HIT is a program for clustering and comparing protein or nucleotide
sequences.  CD-HIT is designed to be fast and handle extremely large
databases.")
    ;; The manual says: "It can be copied under the GNU General Public License
    ;; version 2 (GPLv2)."
    (license license:gpl2)))

(define-public cd-hit-auxtools
  (package
    (inherit cd-hit)
    (name "cd-hit-auxtools")
    (arguments
     (list
      #:tests? #f                       ; there are no tests
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'chdir (lambda _ (chdir "cd-hit-auxtools")))
          ;; No "configure" script
          (delete 'configure)
          ;; There is no install target.
          (replace 'install
            (lambda _
              (for-each (lambda (file)
                          (install-file file (string-append #$output "/bin")))
                        '("cd-hit-dup" "cd-hit-lap" "read-linker")))))))
    (inputs '())))

(define-public clipper
  (package
    (name "clipper")
    (version "2.0.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/YeoLab/clipper")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0508rgnfjk5ar5d1mjbjyrnarv4kw9ksq0m3jw2bmgabmb5v6ikk"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Delete pre-compiled files.
                  (delete-file "clipper/src/peaks.so")))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #false
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'use-python3-for-cython
           (lambda _
             (substitute* "setup.py"
               (("^setup")
                "\
peaks.cython_directives = {'language_level': '3'}
readsToWiggle.cython_directives = {'language_level': '3'}
setup"))))
         (add-after 'unpack 'disable-nondeterministic-test
           (lambda _
             ;; This test fails/succeeds non-deterministically.
             (substitute* "clipper/test/test_call_peak.py"
               (("test_get_FDR_cutoff_mean") "_test_get_FDR_cutoff_mean"))))
         ;; This doesn't work because "usage" is executed, and that calls
         ;; exit(8).
         (replace 'check
           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (with-directory-excursion "clipper/test"
                 (invoke "python" "-m" "unittest")))))
         ;; This is not a library
         (delete 'sanity-check))))
    (inputs
     (list htseq
           python-pybedtools
           python-cython
           python-scikit-learn
           python-matplotlib
           python-pandas
           python-pysam
           python-numpy
           python-scipy))
    (native-inputs
     (list python-setuptools-git
           python-mock ; for tests
           python-nose ; for tests
           python-pytz)) ; for tests
    (home-page "https://github.com/YeoLab/clipper")
    (synopsis "CLIP peak enrichment recognition")
    (description
     "CLIPper is a tool to define peaks in CLIP-seq datasets.")
    (license license:gpl2)))

(define-public codingquarry
  (package
    (name "codingquarry")
    (version "2.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sourceforge/codingquarry/CodingQuarry_v"
                    version ".tar.gz"))
              (sha256
               (base32
                "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;no "check" target
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin"))
                    (doc (string-append #$output "/share/doc/codingquarry")))
                (install-file "INSTRUCTIONS.pdf" doc)
                (copy-recursively "QuarryFiles"
                                  (string-append #$output
                                                 "/share/codingquarry/QuarryFiles"))
                (install-file "CodingQuarry" bin)
                (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
    ;; TODO: This package also needs a Python 2 variant of biopython
    (inputs (list openmpi python-2)) ;Only Python 2 is supported
    (native-search-paths
     (list (search-path-specification
            (variable "QUARRY_PATH")
            (files '("share/codingquarry/QuarryFiles")))))
    (home-page "https://sourceforge.net/projects/codingquarry/")
    (synopsis "Fungal gene predictor")
    (description "CodingQuarry is a highly accurate, self-training GHMM fungal
gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
    (license license:gpl3+)))

(define-public clustal-omega
  (package
    (name "clustal-omega")
    (version "1.2.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://www.clustal.org/omega/clustal-omega-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
    (build-system gnu-build-system)
    (inputs
     (list argtable))
    (home-page "http://www.clustal.org/omega/")
    (synopsis "Multiple sequence aligner for protein and DNA/RNA")
    (description
     "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for protein and DNA/RNA.  It produces high quality MSAs and is capable
of handling data-sets of hundreds of thousands of sequences in reasonable
time.")
    (license license:gpl2+)))

(define-public crossmap
  (package
    (name "crossmap")
    (version "0.6.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "CrossMap" version))
              (sha256
               (base32
                "0hqminh5wn1p3x481jbyc7gmncp5xc196hpvki7k25vzbryhwcix"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Delete compiled Python files.
                  (for-each delete-file (find-files "." "\\.pyc$"))
                  (delete-file-recursively ".eggs")))))
    (build-system python-build-system)
    (inputs
     (list python-bx-python python-numpy python-pybigwig python-pysam
           zlib))
    (native-inputs
     (list python-cython python-nose))
    (home-page "https://crossmap.sourceforge.net/")
    (synopsis "Convert genome coordinates between assemblies")
    (description
     "CrossMap is a program for conversion of genome coordinates or annotation
files between different genome assemblies.  It supports most commonly used
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
    (license license:gpl2+)))

(define-public python-dnaio
  (package
    (name "python-dnaio")
    (version "0.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "dnaio" version))
       (sha256
        (base32
         "064xc4j8plb4fpkm8mw55715mvpvi2sxsknpjx18c2zh904salfy"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:tests? #false)) ;there are none
    (native-inputs
     (list python-cython python-pytest python-setuptools-scm))
    (propagated-inputs
     (list python-xopen))
    (home-page "https://github.com/marcelm/dnaio/")
    (synopsis "Read FASTA and FASTQ files efficiently")
    (description
     "dnaio is a Python library for fast parsing of FASTQ and also FASTA
files.  The code was previously part of the cutadapt tool.")
    (license license:expat)))

(define-public python-deeptoolsintervals
  (package
    (name "python-deeptoolsintervals")
    (version "0.1.9")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "deeptoolsintervals" version))
              (sha256
               (base32
                "1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
    (build-system python-build-system)
    (inputs
     (list zlib))
    (home-page "https://github.com/deeptools/deeptools_intervals")
    (synopsis "Create GTF-based interval trees with associated meta-data")
    (description
     "This package provides a Python module creating/accessing GTF-based
interval trees with associated meta-data.  It is primarily used by the
@code{deeptools} package.")
    (license license:expat)))

(define-public python-deeptools
  (package
    (name "python-deeptools")
    (version "3.5.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/deeptools/deepTools")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0mgcs03amrd5157drbm6ikdg0m0szrn9xbflariz2zrrnqpsai6s"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-test
            (lambda _
              (substitute* "deeptools/test/test_tools.py"
                (("e_ver = _p")
                 "e_ver = \".\" + _p + \"-real\""))
              (substitute* "deeptools/multiBigwigSummary.py"
                (("version='multiBigwigSummary")
                 "version='%(prog)s"))
              (substitute* "deeptools/plotCoverage.py"
                (("version='plotCoverage")
                 "version='%(prog)s")))))))
    (native-inputs
     (list python-mock python-pytest))
    (propagated-inputs
     (list python-matplotlib
           python-numpy
           python-numpydoc
           python-py2bit
           python-pybigwig
           python-pysam
           python-scipy
           python-deeptoolsintervals
           python-plotly))
    (home-page "https://pypi.org/project/deepTools/")
    (synopsis "Useful tools for exploring deep sequencing data")
    (description "This package addresses the challenge of handling large amounts
of data that are now routinely generated from DNA sequencing centers.
@code{deepTools} contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard bedGraph
and bigWig file formats, that allow comparison between different files.  Finally,
using such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for functional
annotations of the genome.")
    ;; The file deeptools/cm.py is licensed under the BSD license.  The
    ;; remainder of the code is licensed under the MIT license.
    (license (list license:bsd-3 license:expat))))

(define-public cutadapt
  (package
    (name "cutadapt")
    (version "4.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "cutadapt" version))
              (sha256
               (base32
                "0xgsv88mrlw2b1radmd1104y7bg8hvv54ay7xfdpnjiw2jgkrha9"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k" "not test_no_read_only_comment_fasta_input")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-test
            (lambda _
              (let ((site (string-append
                           #$output "/lib/python"
                           #$(version-major+minor
                              (package-version python))
                           "/site-packages")))
                (substitute* "tests/test_command.py"
                  (("env=\\{\"LC_CTYPE\": \"C\"\\},")
                   (string-append "env={\"LC_CTYPE\": \"C\", \"GUIX_PYTHONPATH\": \""
                                  (getenv "GUIX_PYTHONPATH") ":" site
                                  "\"},")))))))))
    (inputs
     (list python-dnaio python-xopen))
    (native-inputs
     (list python-cython
           python-pytest
           python-pytest-mock
           python-pytest-timeout
           python-setuptools-scm))
    (home-page "https://cutadapt.readthedocs.io/en/stable/")
    (synopsis "Remove adapter sequences from nucleotide sequencing reads")
    (description
     "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
other types of unwanted sequence from high-throughput sequencing reads.")
    (license license:expat)))

(define-public lammps
  (let ((commit "stable_2Aug2023_update2"))
    (package
      (name "lammps")
      (version (string-append "0." commit))
      (source
       (origin
	 (method git-fetch)
	 (uri (git-reference
	       (url "https://github.com/lammps/lammps.git")
	       (commit commit)))
	 (file-name (git-file-name name version))
	 (sha256
	  (base32
	   "11xagacgxgldkx34qdzyjrjvn8x3hpl0kgzhh9zh7skpq79pwycz"))))
      (build-system gnu-build-system)
      (arguments
       (list
        #:tests? #f                     ; no check target
	#:make-flags
        '(list "CC=mpicc" "mpi"
	       "LMP_INC=-DLAMMPS_GZIP \
-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64"
	       "LIB=-gz -ljpeg -lpng -lavcodec")
	#:phases
	#~(modify-phases %standard-phases
            (add-after 'unpack 'chdir
	      (lambda _ (chdir "src")))
	    (replace 'configure
	      (lambda _
		(substitute* "MAKE/Makefile.mpi"
		  (("SHELL =.*")
		   (string-append "SHELL=" (which "bash") "\n"))
		  (("cc ") "mpicc "))
		(substitute* "Makefile"
		  (("SHELL =.*")
		   (string-append "SHELL=" (which "bash") "\n")))))
	    (add-after 'configure 'configure-modules
	      (lambda _
		(invoke "make"
			"yes-molecule"
			"yes-misc"
			"yes-granular"
			(string-append "HDF5_PATH="
				       #$(this-package-input "hdf5")))))
	    (replace 'install
	      (lambda _
		(let ((bin (string-append #$output "/bin")))
		  (mkdir-p bin)
		  (install-file "lmp_mpi" bin)))))))
      (inputs
       (list ffmpeg
	     gfortran
	     gzip
	     hdf5
	     libjpeg-turbo
	     libpng
	     openmpi
             python-wrapper))
      (native-inputs (list bc))
      (home-page "https://www.lammps.org/")
      (synopsis "Classical molecular dynamics simulator")
      (description "LAMMPS is a classical molecular dynamics simulator
designed to run efficiently on parallel computers.  LAMMPS has potentials for
solid-state materials (metals, semiconductors), soft matter (biomolecules,
polymers), and coarse-grained or mesoscopic systems.  It can be used to model
atoms or, more generically, as a parallel particle simulator at the atomic,
meso, or continuum scale.")
      (license license:gpl2+))))

(define-public lammps-serial
  (package
    (inherit lammps)
    (name "lammps-serial")
    (arguments
     (substitute-keyword-arguments (package-arguments lammps)
       ((#:make-flags flags)
        '(list "CC=gcc" "serial"
               "LMP_INC=-DLAMMPS_GZIP \
-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64"
               "LIB=-gz -ljpeg -lpng -lavcodec"))
       ((#:phases phases)
        #~(modify-phases #$phases
            (replace 'configure
              (lambda _
                (substitute* "MAKE/Makefile.serial"
                  (("SHELL =.*")
                   (string-append "SHELL=" (which "bash") "\n"))
                  (("cc ") "gcc "))
                (substitute* "Makefile"
                  (("SHELL =.*")
                   (string-append "SHELL=" (which "bash") "\n")))))
            (replace 'install
	      (lambda _
		(let ((bin (string-append #$output "/bin")))
		  (mkdir-p bin)
		  (install-file "lmp_serial" bin))))))))
    (inputs
     (modify-inputs (package-inputs lammps)
       (delete "openmpi")))))

(define-public libbigwig
  (package
    (name "libbigwig")
    (version "0.4.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dpryan79/libBigWig")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "09693dmf1scdac5pyq6qyn8b4mcipvnmc370k9a5z41z81m3dcsj"))))
    (build-system gnu-build-system)
    (arguments
     `(#:test-target "test"
       #:tests? #f ; tests require access to the web
       #:make-flags
       ,#~(list "CC=gcc"
                (string-append "prefix=" #$output))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (inputs
     (list zlib curl))
    (native-inputs
     `(("doxygen" ,doxygen)
       ;; Need for tests
       ("python" ,python-2)))
    (home-page "https://github.com/dpryan79/libBigWig")
    (synopsis "C library for handling bigWig files")
    (description
     "This package provides a C library for parsing local and remote BigWig
files.")
    (license license:expat)))

(define-public lsgkm
  (package
    (name "lsgkm")
    (version "0.1.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/Dongwon-Lee/lsgkm.git")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0b3m94kndvimdfjaf1q2yhmsn7lm5s9v81c5xgfjcp6ig7mh3sa5"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:make-flags '(list "-C" "src")
      #:tests? #false                   ;there are no executable tests
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin")))
                (for-each (lambda (file)
                            (install-file file bin))
                          '("src/gkmtrain"
                            "src/gkmpredict"))))))))
    (home-page "https://github.com/Dongwon-Lee/lsgkm")
    (synopsis "Predict regulatory DNA elements in large-scale data")
    (description "gkm-SVM, a sequence-based method for predicting regulatory
DNA elements, is a useful tool for studying gene regulatory mechanisms.
LS-GKM is an effort to improve the method.  It offers much better scalability
and provides further advanced gapped k-mer based kernel functions.  As a
result, LS-GKM achieves considerably higher accuracy than the original
gkm-SVM.")
    (license license:gpl3+)))

(define-public python-fcsparser
  (package
    (name "python-fcsparser")
    (version "0.2.8")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "fcsparser" version))
       (sha256
        (base32 "1skk1k8phq9sj4ar0cnq8px89y3kcyh5zrbl6anz9wcdcyzkc16z"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-numpy python-pandas))
    (native-inputs (list python-poetry-core python-pytest))
    (home-page "https://github.com/eyurtsev/fcsparser")
    (synopsis "Package for reading raw fcs files")
    (description
     "This package provides a Python package for reading raw fcs files")
    (license license:expat)))

(define-public python-pybigwig
  (package
    (name "python-pybigwig")
    (version "0.3.22")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pyBigWig" version))
              (sha256
               (base32
                "0hr25lkp26mk0fp7irdjdrdsd5lann9kyv0xq9npyyxxakvjci2x"))
              (modules '((guix build utils)))
              (snippet
               ;; Delete bundled libBigWig sources
               '(delete-file-recursively "libBigWig"))))
    (build-system pyproject-build-system)
    (arguments
     '(#:tests? #false      ;only one test exists and it needs internet access
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'link-with-libBigWig
           (lambda _
             (substitute* "setup.py"
               (("libs=\\[") "libs=[\"BigWig\", ")))))))
    (propagated-inputs
     (list python-numpy))
    (inputs
     (list libbigwig zlib curl))
    (home-page "https://github.com/dpryan79/pyBigWig")
    (synopsis "Access bigWig files in Python using libBigWig")
    (description
     "This package provides Python bindings to the libBigWig library for
accessing bigWig files.")
    (license license:expat)))

(define-public python-pyfasta
  ;; The release on pypi does not contain the test data files.
  (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03")
        (revision "1"))
    (package
      (name "python-pyfasta")
      (version (git-version "0.5.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/brentp/pyfasta")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7"))))
      (build-system pyproject-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'python3.10-compat
             (lambda _
               (substitute* "pyfasta/__init__.py"
                 (("from fasta import")
                  "from pyfasta.fasta import")
                 (("from records import")
                  "from pyfasta.records import")
                 (("from split_fasta import")
                  "from pyfasta.split_fasta import")
                 (("in f.iteritems")
                  "in f.items"))
               (substitute* "pyfasta/fasta.py"
                 (("from collections import Mapping")
                  "from collections.abc import Mapping")
                 (("from records import")
                  "from pyfasta.records import"))
               (substitute* "pyfasta/records.py"
                 (("cPickle") "pickle")
                 (("\\(int, long\\)")
                  "(int, int)")
                 ;; XXX: it's not clear if this is really correct.
                 (("buffer\\(self\\)")
                  "memoryview(bytes(str(self), encoding='utf-8'))")
                 (("sys.maxint") "sys.maxsize"))
               (substitute* "pyfasta/split_fasta.py"
                 (("from cStringIO import")
                  "from io import")
                 (("in lens.iteritems") "in lens.items"))
               (substitute* "tests/test_all.py"
                 (("f.keys\\(\\)\\) == \\['a-extra'")
                  "list(f.keys())) == ['a-extra'")
                 (("f.iterkeys\\(\\)") "iter(f.keys())")
                 (("tests/data/" m)
                  (string-append (getcwd) "/" m))))))))
      (propagated-inputs (list python-numpy))
      (native-inputs (list python-nose))
      (home-page "https://github.com/brentp/pyfasta/")
      (synopsis "Pythonic access to fasta sequence files")
      (description
       "This library provides fast, memory-efficient, pythonic (and
command-line) access to fasta sequence files.  It stores a flattened version
of a fasta sequence file without spaces or headers and uses either a
@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the
sequence data is never read into memory.  It saves a pickle (@code{.gdx}) of
the start and stop (for @code{fseek}/@code{mmap}) locations of each header in
the fasta file for internal use.

Note that this package has been deprecated in favor of @code{pyfaidx}.")
      (license license:expat))))

(define-public python-schema-salad
  (package
    (name "python-schema-salad")
    (version "8.5.20240102191335")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "schema-salad" version))
        (sha256
         (base32
          "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'set-version
            (lambda _
              ;; Set exact version.
              (substitute* "setup.py"
                (("use_scm_version=True")
                 (string-append "version=\"" #$version "\"")))))
          (add-before 'check 'skip-failing-tests
            (lambda _
              ;; Skip tests that require network access.
              (let ((skip-test
                     (lambda (test-pattern)
                       (string-append "@pytest.mark.skip(reason="
                                      "\"test requires network access\")\n"
                                      test-pattern))))
                (substitute* "schema_salad/tests/test_cg.py"
                  (("^def test_(load(_by_yaml_metaschema|_metaschema|_cwlschema|)|include|idmap|idmap2)\\(" all)
                   (skip-test all)))
                (substitute* "schema_salad/tests/test_cwl11.py"
                  (("^def test_(secondaryFiles|outputBinding|yaml_tab_error)\\(" all)
                   (skip-test all)))
                (substitute* "schema_salad/tests/test_examples.py"
                  (("^def test_bad_schemas\\(" all)
                   (skip-test all)))))))))
    (propagated-inputs
     (list python-cachecontrol
           python-importlib-resources
           python-mistune-next
           python-mypy-extensions
           python-rdflib
           python-requests
           python-ruamel.yaml))
    (native-inputs
     (list python-black python-pytest python-pytest-runner python-pytest-xdist))
    (home-page "https://github.com/common-workflow-language/schema_salad")
    (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
    (description
     "Salad is a schema language for describing JSON or YAML structured linked
data documents.  Salad schema describes rules for preprocessing, structural
validation, and hyperlink checking for documents described by a Salad schema.
Salad supports rich data modeling with inheritance, template specialization,
object identifiers, object references, documentation generation, code
generation, and transformation to RDF.  Salad provides a bridge between document
and record oriented data modeling and the Semantic Web.")
    (license license:asl2.0)))

(define-public python-scikit-bio
  (package
    (name "python-scikit-bio")
    (version "0.6.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "scikit-bio" version))
              (sha256
               (base32
                "03y1n91p6m44hhxm3rpb355j6ddalydz49s94h85kbhm7iy5l40h"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; Accuracy problem
      '(list "-k" (string-append "not test_fisher_alpha"
                                 ;; UNEXPECTED EXCEPTION: ValueError("could
                                 ;; not convert string to float: 'gut'")
                                 " and not skbio.diversity"))
      #:phases
      '(modify-phases %standard-phases
         (add-before 'check 'build-extensions
           (lambda _
             ;; Cython extensions have to be built before running the tests.
             (invoke "python3" "setup.py" "build_ext" "--inplace")))
         (replace 'check
           (lambda* (#:key tests? test-flags #:allow-other-keys)
             (when tests?
               (apply invoke "python3" "-m" "skbio.test" test-flags)))))))
    (propagated-inputs
     (list python-biom-format
           python-decorator
           python-h5py
           python-hdmedians
           python-natsort
           python-numpy
           python-pandas
           python-requests
           python-scipy))
    (native-inputs
     (list python-coverage python-pytest))
    (home-page "https://scikit-bio.org")
    (synopsis "Data structures, algorithms and educational resources for bioinformatics")
    (description
     "This package provides data structures, algorithms and educational
resources for bioinformatics.")
    (license license:bsd-3)))

(define-public python-scrublet
  (package
    (name "python-scrublet")
    (version "0.2.3")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "scrublet" version))
              (sha256
               (base32
                "0fk5pwk12yz9wpvwkl6j2l2g28f3x35b9r9n5bw6f0i9f0qgd191"))))
    (build-system pyproject-build-system)
    (arguments '(#:tests? #false)) ;there are none
    (propagated-inputs
     (list python-annoy
           python-cython
           python-matplotlib
           python-numba
           python-numpy
           python-pandas
           python-scikit-image
           python-scikit-learn
           python-scipy
           python-umap-learn))
    (home-page "https://github.com/swolock/scrublet")
    (synopsis "Tool to indentify and remove doublets in single-cell data")
    (description "This package provides a tool for identifying and removing
doublets in single-cell RNA-seq data.")
    (license license:expat)))

(define-public python-cwlformat
  (package
    (name "python-cwlformat")
    (version "2022.02.18")
    (source
     ;; The PyPI tarball is missing Readme.md. Readme.md is required for the
     ;; build.
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/rabix/cwl-format")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-importlib-resources
           python-ruamel.yaml))
    (home-page "https://github.com/rabix/cwl-format")
    (synopsis "Prettifier for CWL code")
    (description "@code{python-cwlformat} is a specification and a reference
implementation for a very opinionated @acronym{CWL, Common Workflow Language}
code formatter.  It outputs CWL in a standardized YAML format.")
    (license license:asl2.0)))

(define-public python-cwl-upgrader
  (package
    (name "python-cwl-upgrader")
    (version "1.2.11")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cwl-upgrader" version))
       (sha256
        (base32
         "12j6z8nvwnzjjyypz59hwj5hmrcri2r6aknw52n9dbj6lbzbdd2p"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-pytest))
    (propagated-inputs
     (list python-ruamel.yaml
           python-schema-salad))
    (home-page "https://github.com/common-workflow-language/cwl-upgrader")
    (synopsis "CWL document upgrader")
    (description "@code{python-cwl-upgrader} is a standalone upgrader for
@acronym{CWL, Common Workflow Language} documents from version draft-3, v1.0,
and v1.1 to v1.2.")
    (license license:asl2.0)))

(define-public python-cwl-utils
  (package
    (name "python-cwl-utils")
    (version "0.32")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cwl-utils" version))
       (sha256
        (base32
         "06wkw8d8cqm3hnz8xwnysz874gwaym36c358cr7frw5iglhvsj98"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      #~(list "-k"
              (string-append "not test_graph_split"
                             " and not test_load_document_with_remote_uri"
                             " and not test_remote_packing"
                             " and not test_remote_packing_github_soft_links"
                             " and not test_value_from_two_concatenated_expressions"))))
    (inputs
     (list node))
    (native-inputs
     (list python-mypy-extensions
           python-pytest
           python-pytest-mock
           python-pytest-runner))
    (propagated-inputs
     (list python-cwl-upgrader
           python-cwlformat
           python-packaging
           python-rdflib
           python-requests
           python-ruamel.yaml
           python-schema-salad))
    (home-page "https://github.com/common-workflow-language/cwl-utils")
    (synopsis "Python utilities for CWL")
    (description "@code{python-cwl-utils} provides python utilities and
autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2
documents.")
    (license license:asl2.0)))

(define-public cwltool
  (package
    (name "cwltool")
    (version "3.1.20240112164112")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/common-workflow-language/cwltool")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'loosen-version-restrictions
            (lambda _
              (substitute* "setup.py"
                (("== 1.5.1") "> 1.5.1")))) ; prov
          (add-after 'unpack 'set-version
            (lambda _
              ;; Set exact version.
              (substitute* "setup.py"
                (("use_scm_version=True")
                 (string-append "version=\"" #$version "\"")))))
          (add-after 'unpack 'modify-tests
            (lambda _
              ;; Tries to connect to the internet.
              (delete-file "tests/test_content_type.py")
              (delete-file "tests/test_udocker.py")
              (delete-file "tests/test_http_input.py")
              (substitute* "tests/test_load_tool.py"
                (("def test_load_graph_fragment_from_packed")
                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
                                "def test_load_graph_fragment_from_packed")))
              (substitute* "tests/test_examples.py"
                (("def test_env_filtering")
                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
                                "def test_env_filtering")))
              ;; Tries to use cwl-runners.
              (substitute* "tests/test_examples.py"
                (("def test_v1_0_arg_empty_prefix_separate_false")
                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
                                "def test_v1_0_arg_empty_prefix_separate_false")))
              (substitute* '("tests/subgraph/env-tool2.cwl"
                             "tests/subgraph/env-tool2_req.cwl"
                             "tests/subgraph/env-wf2_subwf-packed.cwl"
                             "tests/subgraph/env-tool2_no_env.cwl")
                (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))))))))
    (inputs
     (list python-argcomplete
           python-bagit
           python-coloredlogs
           python-cwl-utils
           python-mypy-extensions
           python-prov
           python-pydot
           python-psutil
           python-rdflib-6
           python-requests
           python-ruamel.yaml
           python-schema-salad
           python-shellescape
           python-spython
           python-typing-extensions
           ;; Not listed as needed but still necessary:
           node))
    (native-inputs
     (list python-arcp
           python-humanfriendly
           python-mock
           python-pytest
           python-pytest-cov
           python-pytest-mock
           python-pytest-runner
           python-pytest-xdist))
    (home-page
     "https://github.com/common-workflow-language/common-workflow-language")
    (synopsis "Common Workflow Language reference implementation")
    (description
     "This is the reference implementation of the @acronym{CWL, Common Workflow
Language} standards.  The CWL open standards are for describing analysis
workflows and tools in a way that makes them portable and scalable across a
variety of software and hardware environments, from workstations to cluster,
cloud, and high performance computing (HPC) environments.  CWL is designed to
meet the needs of data-intensive science, such as Bioinformatics, Medical
Imaging, Astronomy, Physics, and Chemistry.  The @acronym{cwltool, CWL reference
implementation} is intended to be feature complete and to provide comprehensive
validation of CWL files as well as provide other tools related to working with
CWL descriptions.")
    (license license:asl2.0)))

(define-public python-dendropy
  (package
    (name "python-dendropy")
    (version "4.5.1")
    (source
     (origin
       (method git-fetch)
       ;; Source from GitHub so that tests are included.
       (uri (git-reference
             (url "https://github.com/jeetsukumaran/DendroPy")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0lrfzjqzbpk1rrra9vd7z2j7q09jy9w1ss7wn2rd85i4k5y3xz8l"))))
    (build-system pyproject-build-system)
    (arguments
     (list
       #:test-flags
       '(list "-k"
              (string-join
               ;; These tests fail because we have no "paup" executable.
               (list "not test_group1"
                     "test_basic_split_counting_under_different_rootings"
                     "test_basic_split_count_with_incorrect_weight_treatment_raises_error"
                     "test_basic_split_count_with_incorrect_rootings_raises_error"

                     ;; Assert error for unknown reasons
                     "test_by_num_lineages")
               " and not "))
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'python-compatibility
            (lambda _
              (substitute* "tests/test_datamodel_taxon.py"
                (("collections.Iterable")
                 "collections.abc.Iterable")))))))
    (native-inputs (list python-pytest))
    (home-page "https://dendropy.org/")
    (synopsis "Library for phylogenetics and phylogenetic computing")
    (description
     "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
writing, simulation, processing and manipulation of phylogenetic
trees (phylogenies) and characters.")
    (license license:bsd-3)))

(define-public python-py2bit
  (package
    (name "python-py2bit")
    (version "0.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "py2bit" version))
       (sha256
        (base32
         "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5"))))
    (build-system python-build-system)
    (home-page "https://github.com/dpryan79/py2bit")
    (synopsis "Access 2bit files using lib2bit")
    (description
     "This package provides Python bindings for lib2bit to access 2bit files
with Python.")
    (license license:expat)))

(define-public delly
  (package
    (name "delly")
    (version "0.8.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dellytools/delly")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
              (modules '((guix build utils)))
              (snippet
               '(delete-file-recursively "src/htslib"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;There are no tests to run.
      #:make-flags
      #~(list "PARALLEL=1"             ; Allow parallel execution at run-time.
              (string-append "prefix=" #$output))
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)           ; There is no configure phase.
          (add-after 'install 'install-templates
            (lambda _
              (let ((templates (string-append #$output
                                              "/share/delly/templates")))
                (mkdir-p templates)
                (copy-recursively "excludeTemplates" templates)))))))
    (inputs
     (list boost bzip2 htslib zlib))
    (home-page "https://github.com/dellytools/delly")
    (synopsis "Integrated structural variant prediction method")
    (description "Delly is an integrated structural variant prediction method
that can discover and genotype deletions, tandem duplications, inversions and
translocations at single-nucleotide resolution in short-read massively parallel
sequencing data.  It uses paired-ends and split-reads to sensitively and
accurately delineate genomic rearrangements throughout the genome.")
    (license license:gpl3+)))

(define-public transanno
  (package
    (name "transanno")
    (version "0.3.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/informationsea/transanno")
             ;; Corresponds to tag v0.3.0
             (commit "df49050c92644ea12d9d5c6fae2186ca436dbca3")))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1jpn7s3cnd9ybk4lmfbhj2arhf6cmrv7jp74n7n87m3a3irkaif1"))
       (snippet
        '(with-output-to-file "liftover-rs/build.rs"
           (lambda _
             (format #true
                     "fn main() {~@
                        println!(\"cargo:rustc-link-lib=lzma\");~@
                        }~%"))))))
    (build-system cargo-build-system)
    (arguments
     (list
      #:install-source? #false          ;fails
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'prepare-test-files
            (lambda _
              (delete-file "Cargo.lock")
              (substitute* "liftover-rs/prepare-test.sh"
                (("/bin/bash")
                 (string-append #$(this-package-native-input "bash")
                                "/bin/bash")))
              (invoke "bash" "prepare-test-files.sh")))
          (add-before 'install 'chdir
            (lambda _ (chdir "transanno"))))
      #:cargo-inputs
      `(("rust-anyhow" ,rust-anyhow-1)
        ("rust-autocompress" ,rust-autocompress-0.2)
        ("rust-bio" ,rust-bio-0.41)
        ("rust-clap" ,rust-clap-2)
        ("rust-csv" ,rust-csv-1)
        ("rust-flate2" ,rust-flate2-1)
        ("rust-indexmap" ,rust-indexmap-1)
        ("rust-log" ,rust-log-0.4)
        ("rust-nom" ,rust-nom-5)
        ("rust-once-cell" ,rust-once-cell-1)
        ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3)
        ("rust-regex" ,rust-regex-1)
        ("rust-thiserror" ,rust-thiserror-1)
        ("rust-serde" ,rust-serde-1)
        ("rust-serde-json" ,rust-serde-json-1))
      #:cargo-development-inputs
      `(("rust-clap" ,rust-clap-2)
        ("rust-lazy-static" ,rust-lazy-static-1))))
    (native-inputs (list bash pkg-config))
    (inputs (list xz))
    (home-page "https://github.com/informationsea/transanno")
    (synopsis "LiftOver tool for new genome assemblies")
    (description "This package provides an accurate VCF/GFF3/GTF LiftOver tool
for new genome assemblies.")
    (license license:gpl3+)))

(define-public trf
  (package
    (name "trf")
    (version "4.09.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/Benson-Genomics-Lab/TRF")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32 "0fhwr4s1mf8nw8fr5imwjvjr42b59p97zr961ifm8xl1bajz4wpg"))))
    (build-system gnu-build-system)
    (home-page "https://github.com/Benson-Genomics-Lab/TRF")
    (synopsis "Tandem Repeats Finder: a program to analyze DNA sequences")
    (description "A tandem repeat in DNA is two or more adjacent, approximate
copies of a pattern of nucleotides.  Tandem Repeats Finder is a program to
locate and display tandem repeats in DNA sequences.  In order to use the
program, the user submits a sequence in FASTA format.  The output consists of
two files: a repeat table file and an alignment file.  Submitted sequences may
be of arbitrary length. Repeats with pattern size in the range from 1 to 2000
bases are detected.")
    (license license:agpl3+)))

(define-public trinityrnaseq
  (package
    (name "trinityrnaseq")
    (version "2.13.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/trinityrnaseq/trinityrnaseq.git")
                    (commit (string-append "Trinity-v" version))
                    (recursive? #true)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1qszrxqbx4q5pavpgm4rkrh1z1v1mf7qx83vv3fnlqdmncnsf1gv"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:test-target "test"
      #:modules
      '((guix build gnu-build-system)
        (guix build utils)
        (ice-9 match)
        (srfi srfi-1))
      #:make-flags
      #~(list (string-append "CC=" #$(cc-for-target)))
      #:phases
      #~(modify-phases %standard-phases
          (replace 'configure
            (lambda _
              (setenv "SHELL" (which "sh"))
              (setenv "CONFIG_SHELL" (which "sh"))
              ;; Do not require version.h, which triggers a local build of a
              ;; vendored htslib.
              (substitute* "trinity-plugins/bamsifter/Makefile"
                (("sift_bam_max_cov.cpp htslib/version.h")
                 "sift_bam_max_cov.cpp"))))
          (add-after 'build 'build-plugins
            (lambda _
              ;; Run this in the subdirectory to avoid running the
              ;; tests right here.
              (with-directory-excursion "trinity-plugins"
                (invoke "make" "plugins"))))
          ;; The install script uses rsync, provides no overrides for the
          ;; default location at /usr/local/bin, and patching it would change
          ;; all lines that do something.
          (replace 'install
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((share (string-append #$output "/share/trinity/"))
                    (bin   (string-append #$output "/bin/")))
                (mkdir-p bin)
                (copy-recursively "." share)
                (delete-file (string-append share "/Chrysalis/build/CMakeFiles/CMakeOutput.log"))
                (delete-file (string-append share "/Inchworm/build/CMakeFiles/CMakeOutput.log"))

                (wrap-program (string-append share "Trinity")
                  `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
                  `("PERL5LIB"    ":" = (,(getenv "PERL5LIB")))
                  `("PYTHONPATH"  ":" = (,(getenv "GUIX_PYTHONPATH")))
                  `("PATH"        ":" =
                    ,(cons (string-append share "/trinity-plugins/BIN")
                           (filter-map (match-lambda
                                         ((name . dir)
                                          (string-append dir "/bin")))
                                       inputs))))
                (symlink (string-append share "Trinity")
                         (string-append bin "Trinity"))))))))
    (inputs
     (list blast+
           bowtie
           fastqc
           hisat
           htslib
           icedtea-8
           jellyfish
           kallisto
           multiqc
           perl
           perl-uri-escape
           python-numpy
           python-wrapper
           r-ape
           r-argparse
           r-biobase
           r-ctc
           r-deseq2
           r-edger
           r-fastcluster
           r-glimma
           r-goplot
           r-goseq
           r-gplots
           r-minimal
           r-qvalue
           r-rots
           r-sm
           r-tidyverse
           rsem
           salmon
           samtools
           sra-tools
           star
           zlib))
    (propagated-inputs
     (list coreutils
           gzip
           which))
    (native-inputs (list cmake))
    (home-page "https://github.com/trinityrnaseq/trinityrnaseq/wiki")
    (synopsis "Trinity RNA-Seq de novo transcriptome assembly")
    (description "Trinity assembles transcript sequences from Illumina RNA-Seq
data.  Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data.  Trinity combines three
independent software modules: Inchworm, Chrysalis, and Butterfly, applied
sequentially to process large volumes of RNA-seq reads.  Trinity partitions
the sequence data into many individual de Bruijn graphs, each representing the
transcriptional complexity at a given gene or locus, and then processes each
graph independently to extract full-length splicing isoforms and to tease
apart transcripts derived from paralogous genes.")
    (license license:bsd-3)))

(define-public repeat-masker
  (package
    (name "repeat-masker")
    (version "4.1.2-p1")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://www.repeatmasker.org/"
                                  "RepeatMasker/RepeatMasker-"
                                  version ".tar.gz"))
              (sha256
               (base32 "15hfdfpzmdjcx7ng7rjfid69bmvgn3z9g9r43qhjnhjhq3v4prab"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #false ; there are none
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'build
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((share (string-append (assoc-ref outputs "out")
                                         "/share/RepeatMasker")))
               (mkdir-p share)
               (copy-recursively "." share)
               (with-directory-excursion share
                 (invoke "perl" "configure"
                         "--trf_prgm" (which "trf")
                         "--hmmer_dir"
                         (string-append (assoc-ref inputs "hmmer")
                                        "/bin"))))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out   (assoc-ref outputs "out"))
                    (share (string-append out "/share/RepeatMasker"))
                    (bin   (string-append out "/bin"))
                    (path  (getenv "PERL5LIB")))
               (install-file (string-append share "/RepeatMasker") bin)
               (wrap-program (string-append bin "/RepeatMasker")
                 `("PERL5LIB" ":" prefix (,path ,share)))))))))
    (inputs
     (list bash-minimal
           perl
           perl-text-soundex
           python
           python-h5py
           hmmer
           trf))
    (home-page "https://github.com/Benson-Genomics-Lab/TRF")
    (synopsis "Tandem Repeats Finder: a program to analyze DNA sequences")
    (description "A tandem repeat in DNA is two or more adjacent, approximate
copies of a pattern of nucleotides.  Tandem Repeats Finder is a program to
locate and display tandem repeats in DNA sequences.  In order to use the
program, the user submits a sequence in FASTA format.  The output consists of
two files: a repeat table file and an alignment file.  Submitted sequences may
be of arbitrary length. Repeats with pattern size in the range from 1 to 2000
bases are detected.")
    (license license:osl2.1)))

(define-public trust4
  (package
    (name "trust4")
    (version "1.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/liulab-dfci/TRUST4")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "170k4rrchg7f2jyn3v4y4fxxq1d49n1vnvhx5xcnnr6jql8q3h08"))
       (modules '((guix build utils)))
       (snippet '(begin
                   ;; Remove bundled samtools
                   (delete-file-recursively "samtools-0.1.19")))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f ;there are no tests
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'use-samtools-headers
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "Makefile"
                (("LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19")
                 (string-append "LINKPATH= -I."
                                #$(this-package-native-input "samtools")
                                "/include/samtools"
                                " -L."
                                #$(this-package-native-input "samtools")
                                "/lib"))
                (("./samtools-0.1.19/")
                 (string-append #$(this-package-native-input
                                   "samtools") "/lib/")))
              (substitute* "alignments.hpp"
                (("samtools-0.1.19")
                 (string-append #$(this-package-native-input
                                   "samtools") "/include/samtools")))))
          (delete 'configure) ; No configure.
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
                    (scripts (string-append #$output
                                            "/share/trust4/scripts")))
                (install-file "annotator" bin)
                (install-file "bam-extractor" bin)
                (install-file "fastq-extractor" bin)
                (install-file "run-trust4" bin)
                (install-file "trust4" bin)
                ;; install scripts stored in the scrips dir
                (for-each (lambda (file)
                            (chmod file #o555))
                          (find-files "scripts" "\\.p(y|l)"))
                (copy-recursively "scripts" scripts)
                (delete-file-recursively "scripts")
                ;; install the rest of the scripts that are in the main dir
                (for-each (lambda (file)
                            (chmod file #o555)
                            (install-file file bin))
                          (find-files "." "\\.(pl|py|sh)"))))))))
    (native-inputs (list automake samtools-0.1))
    (inputs (list perl python-wrapper zlib))
    (home-page "https://github.com/liulab-dfci/TRUST4")
    (synopsis "TCR and BCR assembly from RNA-seq data")
    (description "This package is analyzing @acronym{TCR, T cell receptor} and
@acronym{BCR, B cell receptor} sequences using unselected RNA sequencing data,
profiled from fluid and solid tissues, including tumors.  TRUST4 performs de
novo assembly on V, J, C genes including the hypervariable @acronym{CDR3,
complementarity-determining region 3} and reports consensus contigs of BCR/TCR
sequences.  TRUST4 then realigns the contigs to IMGT reference gene sequences to
identify the corresponding gene and CDR3 details.  TRUST4 supports both single-end
and paired-end bulk or single-cell sequencing data with any read length.")
    (license license:gpl3)))

(define-public diamond
  (package
    (name "diamond")
    (version "2.1.6")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/bbuchfink/diamond")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0kb17jwlsrvgswfahzznrffv1i6ybwwmq99qs7iga5yzbx64jp6q"))))
    (build-system cmake-build-system)
    (arguments
     (list #:configure-flags '(list "-DX86=OFF"))) ;avoid SSE4 and AVX2
    (inputs (list zlib))
    (home-page "https://github.com/bbuchfink/diamond")
    (synopsis "Accelerated BLAST compatible local sequence aligner")
    (description
     "DIAMOND is a BLAST-compatible local aligner for mapping protein and
translated DNA query sequences against a protein reference database (BLASTP
and BLASTX alignment mode).  The speedup over BLAST is up to 20,000 on short
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
data and settings.")
    (license license:gpl3+)))

(define-public discrover
  (package
    (name "discrover")
    (version "1.6.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/maaskola/discrover")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f                      ; there are no tests
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'set-force-source-date
           ;; for reproducible dates, texlive needs this to respect
           ;; SOURCE_DATE_EPOCH
           (lambda _
             (setenv "FORCE_SOURCE_DATE" "1")))
         (add-after 'unpack 'fix-latex-errors
           (lambda _
             (with-fluids ((%default-port-encoding #f))
               (substitute* "doc/references.bib"
                 (("\\{S\\}illanp[^,]+,")
                  "{S}illanp{\\\"a}{\\\"a},")))
             ;; XXX: I just can't get pdflatex to not complain about these
             ;; characters.  They end up in the manual via the generated
             ;; discrover-cli-help.txt.
             (substitute* "src/hmm/cli.cpp"
               (("µ") "mu")
               (("η") "eta")
               (("≤") "<="))
             ;; This seems to be a syntax error.
             (substitute* "doc/discrover-manual.tex"
               (("theverbbox\\[t\\]") "theverbbox"))))
         (add-after 'unpack 'add-missing-includes
           (lambda _
             (substitute* "src/executioninformation.hpp"
               (("#define EXECUTIONINFORMATION_HPP" line)
                (string-append line "\n#include <random>")))
             (substitute* "src/plasma/fasta.hpp"
               (("#define FASTA_HPP" line)
                (string-append line "\n#include <random>"))))))))
    (inputs
     (list boost cairo rmath-standalone))
    (native-inputs
     (list (texlive-updmap.cfg
            (list texlive-doi
                  texlive-examplep
                  texlive-forloop
                  texlive-listofitems
                  texlive-ms
                  texlive-natbib
                  texlive-pgf           ;tikz
                  texlive-readarray
                  texlive-verbatimbox))
           imagemagick))
    (home-page "https://dorina.mdc-berlin.de/public/rajewsky/discrover/")
    (synopsis "Discover discriminative nucleotide sequence motifs")
    (description "Discrover is a motif discovery method to find binding sites
of nucleic acid binding proteins.")
    (license license:gpl3+)))

(define-public eigensoft
  (package
    (name "eigensoft")
    (version "7.2.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/DReichLab/EIG")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k"))
       (modules '((guix build utils)))
       ;; Remove pre-built binaries.
       (snippet '(begin
                   (delete-file-recursively "bin")
                   (mkdir "bin")
                   #t))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                    ; There are no tests.
       #:make-flags '("CC=gcc")
       #:phases
       (modify-phases %standard-phases
         ;; There is no configure phase, but the Makefile is in a
         ;; sub-directory.
         (replace 'configure
           (lambda _ (chdir "src") #t))
         ;; The provided install target only copies executables to
         ;; the "bin" directory in the build root.
         (add-after 'install 'actually-install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin  (string-append out "/bin")))
               (for-each (lambda (file)
                           (install-file file bin))
                         (find-files "../bin" ".*"))
               #t))))))
    (inputs
     (list gsl openblas perl
           `(,gfortran "lib")))
    (home-page "https://github.com/DReichLab/EIG")
    (synopsis "Tools for population genetics")
    (description "The EIGENSOFT package provides tools for population
genetics and stratification correction.  EIGENSOFT implements methods commonly
used in population genetics analyses such as PCA, computation of Tracy-Widom
statistics, and finding related individuals in structured populations.  It
comes with a built-in plotting script and supports multiple file formats and
quantitative phenotypes.")
    ;; The license of the eigensoft tools is Expat, but since it's
    ;; linking with the GNU Scientific Library (GSL) the effective
    ;; license is the GPL.
    (license license:gpl3+)))

(define-public eddylab-squid
  (package
    (name "eddylab-squid")
    (version "1.9g")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://eddylab.org/software/squid/squid-"
                           version ".tar.gz"))
       (sha256
        (base32
         "19ywv1h581a84yyjnp64gwww99vhgbxi8v4rl37xp92ag7l44brh"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'check 'set-perl-search-path
           (lambda _
             ;; Work around "dotless @INC" build failure.
             (setenv "PERL5LIB"
                     (string-append (getcwd) "/Testsuite:"
                                    (getenv "PERL5LIB"))))))))
    (inputs (list perl))
    (home-page "http://eddylab.org/software.html")
    (synopsis "C function library for sequence analysis")
    (description "SQUID is Sean Eddy's personal library of C functions
and utility programs for sequence analysis.")
    (license license:gpl2)))

(define-public edirect
  (package
    (name "edirect")
    (version "13.3.20200128")
    (source (origin
              (method url-fetch)
              (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
                                  "/versions/" version
                                  "/edirect-" version ".tar.gz"))
              (sha256
               (base32
                "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33"))
              (modules '((guix build utils)))
              (snippet
               '(begin (delete-file "Mozilla-CA.tar.gz")
                       (substitute* "rchive.go"
                         ;; This go library does not have any license.
                         (("github.com/fiam/gounidecode/unidecode")
                          "golang.org/rainycape/unidecode"))))))
    (build-system perl-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build)
         (delete 'check)                ; simple check after install
         (add-after 'unpack 'patch-programs
           (lambda* (#:key inputs #:allow-other-keys)
             ;; Ignore errors about missing xtract.Linux and rchive.Linux.
              (substitute* "pm-refresh"
                (("cat \\\"\\$target")
                 "grep ^[[:digit:]] \"$target"))))
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
                   (edirect-go (assoc-ref inputs "edirect-go-programs")))
               (for-each
                 (lambda (file)
                   (install-file file bin))
                 '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
                   "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
                   "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
                   "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
                   "pm-index" "pm-invert" "pm-merge" "pm-promote"))
               (symlink (string-append edirect-go "/bin/xtract.Linux")
                        (string-append bin "/xtract"))
               (symlink (string-append edirect-go "/bin/rchive.Linux")
                        (string-append bin "/rchive")))))
         (add-after 'install 'wrap-program
           (lambda* (#:key outputs #:allow-other-keys)
              ;; Make sure everything can run in a pure environment.
              (let ((out (assoc-ref outputs "out"))
                    (path (getenv "PERL5LIB")))
                (for-each
                  (lambda (file)
                    (wrap-program file
                      `("PERL5LIB" ":" prefix (,path)))
                    (wrap-program file
                      `("PATH" ":" prefix (,(string-append out "/bin")
                                           ,(dirname (which "sed"))
                                           ,(dirname (which "gzip"))
                                           ,(dirname (which "grep"))
                                           ,(dirname (which "perl"))
                                           ,(dirname (which "uname"))))))
                  (find-files out ".")))))
         (add-after 'wrap-program 'check
           (lambda* (#:key outputs #:allow-other-keys)
             (invoke (string-append (assoc-ref outputs "out")
                                    "/bin/edirect.pl")
                     "-filter" "-help"))))))
    (inputs
     (list bash-minimal
           edirect-go-programs
           perl-html-parser
           perl-encode-locale
           perl-file-listing
           perl-html-tagset
           perl-html-tree
           perl-http-cookies
           perl-http-date
           perl-http-message
           perl-http-negotiate
           perl-lwp-mediatypes
           perl-lwp-protocol-https
           perl-net-http
           perl-uri
           perl-www-robotrules
           perl-xml-simple
           perl))
    (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/")
    (synopsis "Tools for accessing the NCBI's set of databases")
    (description
     "Entrez Direct (EDirect) is a method for accessing the National Center
for Biotechnology Information's (NCBI) set of interconnected
databases (publication, sequence, structure, gene, variation, expression,
etc.) from a terminal.  Functions take search terms from command-line
arguments.  Individual operations are combined to build multi-step queries.
Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the
extraction of data from document summaries or other results that are returned
in structured XML format.  This can eliminate the need for writing custom
software to answer ad hoc questions.")
    (native-search-paths
     ;; Ideally this should be set for LWP somewhere.
     (list (search-path-specification
            (variable "PERL_LWP_SSL_CA_FILE")
            (file-type 'regular)
            (separator #f)
            (files '("/etc/ssl/certs/ca-certificates.crt")))))
    (license license:public-domain)))

(define-public edirect-go-programs
  (package
    (inherit edirect)
    (name "edirect-go-programs")
    (build-system go-build-system)
    (arguments
     `(#:install-source? #f
       #:tests? #f      ; No tests.
       #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
       #:phases
       (modify-phases %standard-phases
         (replace 'build
           (lambda* (#:key import-path #:allow-other-keys)
             (with-directory-excursion (string-append "src/" import-path)
               (invoke "go" "build" "-v" "-x" "j2x.go")
               (invoke "go" "build" "-v" "-x" "t2x.go")
               (invoke "go" "build" "-v" "-x" "-o"
                       "xtract.Linux" "xtract.go" "common.go")
               (invoke "go" "build" "-v" "-x" "-o"
                       "rchive.Linux" "rchive.go" "common.go")
               (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
         (replace 'install
           (lambda* (#:key outputs import-path #:allow-other-keys)
             (let ((dest    (string-append (assoc-ref outputs "out") "/bin"))
                   (source  (string-append "src/" import-path "/")))
               (for-each (lambda (file)
                           (format #t "installing ~a~%" file)
                           (install-file (string-append source file) dest))
                         '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
               #t))))))
    (native-inputs '())
    (propagated-inputs '())
    (inputs
     (list go-github-com-fatih-color
           go-github-com-fogleman-gg
           go-github-com-gedex-inflector
           go-github-com-golang-freetype
           go-github-com-klauspost-cpuid
           go-github-com-pbnjay-memory
           go-github-com-surgebase-porter2
           go-golang-org-rainycape-unidecode
           go-golang-org-x-image
           go-golang-org-x-text))))

(define-public python-baltica
  (package
    (name "python-baltica")
    (version "1.1.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dieterich-lab/Baltica")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               ;; The tests need to be run from elsewhere...
               (mkdir-p "/tmp/test")
               (copy-recursively ".tests" "/tmp/test")
               (with-directory-excursion "/tmp/test"
                 (invoke "pytest" "-v" "--doctest-modules"))))))))
    (propagated-inputs
     (list gunicorn
           python-anndata
           python-click
           python-flask
           python-flask-wtf
           python-h5py
           python-numpy
           python-psutil
           python-pysam
           python-pyyaml
           python-scipy
           r-biocmanager
           r-dplyr
           r-genomicranges
           r-here
           r-openxlsx
           r-optparse
           r-readr
           r-rsamtools
           r-stringr
           r-tidyr
           r-upsetr
           r-yaml
           snakemake-7))
    (native-inputs (list python-cython python-pyfakefs python-pytest))
    (home-page "https://github.com/dieterich-lab/Baltica")
    (synopsis "Integrated splice junction usage analysis")
    (description
     "This framework facilitates the execution of @dfn{differential junction
usage} (DJU) methods.  Additionally, it enables the integration of results from
multiple DJU methods.")
    (license license:expat)))

(define-public python-bamnostic
  (package
    (name "python-bamnostic")
    (version "1.1.8")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "bamnostic" version))
              (sha256
               (base32
                "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-pytest))
    (home-page "https://github.com/betteridiot/bamnostic/")
    (synopsis "Tool for binary alignment map, random access and parsing")
    (description
     "Bamnostic is a pure Python @dfn{Binary Alignment Map} (BAM) file parser
and random access tool.")
    (license license:bsd-3)))

(define-public python-episcanpy
  (package
    (name "python-episcanpy")
    (version "0.4.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "episcanpy" version))
              (sha256
               (base32
                "1qqcyhyzy6idpjmidfdpzwk02hbxm25rymz42h51nlk0vd4r2wwm"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      ;; The tests import episcanpy.api, but this is known to not work.
      ;; See https://github.com/colomemaria/epiScanpy/issues/133
      #:tests? #false
      #:phases
      '(modify-phases %standard-phases
         ;; Numba needs a writable dir to cache functions.
         (add-before 'build 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs
     (list python-anndata
           python-bamnostic
           python-h5py
           python-intervaltree
           python-joblib
           python-kneed
           python-legacy-api-wrap
           python-matplotlib
           python-natsort
           python-networkx
           python-numba
           python-numpy
           python-packaging
           python-pandas
           python-scanpy
           python-scikit-learn
           python-scipy
           python-seaborn
           python-statsmodels
           python-tqdm
           python-pysam
           python-tbb
           python-umap-learn))
    (native-inputs (list python-pytest python-setuptools-scm))
    (home-page "https://github.com/colomemaria/epiScanpy")
    (synopsis "Tool for epigenomics single cell analysis")
    (description
     "EpiScanpy is a toolkit to analyse single-cell open
chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq)
data.  EpiScanpy is the epigenomic extension of the very popular scRNA-seq
analysis tool Scanpy (Genome Biology, 2018).")
    (license license:bsd-3)))

(define-public python-ete3
  (package
    (name "python-ete3")
    (version "3.1.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/etetoolkit/ete")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1i6533wsm06mz0sdrisqai929j744cnczwjgsmxl847q5k16kngd"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             ;; This test crashes Python in the build container
             (string-append "not test_renderer"
                            ;; These all need internet access
                            " and not test_00_update_database"
                            " and not test_01tree_annotation"
                            " and not test_get_topology"
                            " and not test_merged_id"
                            " and not test_ncbi_compare"
                            " and not test_ncbiquery")
             "ete3/test/test_api.py")))
    (propagated-inputs
     (list python-lxml
           python-numpy
           python-pyqt
           python-scipy))
    (native-inputs
     (list python-pytest))
    (home-page "http://etetoolkit.org")
    (synopsis "Python environment for phylogenetic tree exploration")
    (description
     "This package provides a Python environment for phylogenetic tree
exploration.")
    (license license:gpl3+)))

(define-public python-illumina-utils
  (package
    (name "python-illumina-utils")
    (version "2.12")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "illumina-utils" version))
              (sha256
               (base32
                "0z9g0prj7pmgl5z4vdpxv3v30grzhc194801qnf0wqzgy7w3aj2s"))))
    (build-system pyproject-build-system)
    (arguments (list #:tests? #false))  ;there are none
    (propagated-inputs (list python-matplotlib python-numpy python-levenshtein))
    (home-page "https://github.com/meren/illumina-utils")
    (synopsis "Library and scripts to work with Illumina paired-end data")
    (description
     "This package provides a library and collection of scripts to work with
Illumina paired-end data (for CASAVA 1.8+).")
    (license license:gpl2+)))

(define-public python-pyani
  (package
    (name "python-pyani")
    (version "0.2.12")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pyani" version))
              (sha256
               (base32
                "124kdg7168nbh4a5wisfws1fgkd89dd4js9v6dml2lvgclbv4mjg"))))
    (build-system pyproject-build-system)
    ;; This contains two test data files but no way to run the tests.
    (arguments (list #:tests? #false))
    (propagated-inputs
     (list python-biopython python-matplotlib python-pandas
           python-scipy python-seaborn))
    (home-page "https://widdowquinn.github.io/pyani/")
    (synopsis "Calculate genome-scale average nucleotide identity")
    (description
     "Pyani provides a package and script for calculation of genome-scale
average nucleotide identity.")
    (license license:expat)))

(define-public python-pyahocorasick
  (package
    (name "python-pyahocorasick")
    (version "2.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/WojciechMula/pyahocorasick")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1fsnivwcw56q7lwz41c5kbfvxv0v17mmkx43i2a293l49fxj08j8"))))
    (build-system pyproject-build-system)
    (native-inputs (list python-pytest python-twine python-wheel))
    (home-page "https://github.com/WojciechMula/pyahocorasick")
    (synopsis "Library for finding multiple key strings in text")
    (description
     "Pyahocorasick is a fast, memory-efficient library for multi-pattern string search.
This means that you can find multiple key strings occurrences
at once in some input text.")
    (license license:bsd-3)))

(define-public exonerate
  (package
    (name "exonerate")
    (version "2.4.0")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append
         "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
         "exonerate-" version ".tar.gz"))
       (sha256
        (base32
         "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
    (native-inputs
     (list pkg-config))
    (inputs
     (list glib))
    (home-page
     "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
    (synopsis "Generic tool for biological sequence alignment")
    (description
     "Exonerate is a generic tool for pairwise sequence comparison.  It allows
the alignment of sequences using a many alignment models, either exhaustive
dynamic programming or a variety of heuristics.")
    (license license:gpl3)))

(define-public express
  (package
    (name "express")
    (version "1.5.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/adarob/eXpress")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "18nb22n7x820fzjngf4qgyb3mspqkw7xyk7v7s5ps6wfrd8qwscb"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:tests? #f                     ;no "check" target
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "CMakeLists.txt"
                (("set\\(Boost_USE_STATIC_LIBS ON\\)")
                 "set(Boost_USE_STATIC_LIBS OFF)")
                (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
                 (search-input-directory inputs "/include/bamtools"))
                (("\\$\\{PROJECT_SOURCE_DIR\\}/bamtools/lib/libbamtools.a")
                 (search-input-file inputs "/lib/libbamtools.so"))
                (("libbamtools.a") "libbamtools.so"))
              (substitute* "src/CMakeLists.txt"
                (("libprotobuf.a") "libprotobuf.so"))))
          (add-after 'unpack 'remove-update-check
            (lambda _
              (substitute* "src/main.cpp"
                (("#include \"update_check.h\"") "")
                (("check_version\\(PACKAGE_VERSION\\);") "")))))))
    (inputs
     (list boost bamtools protobuf zlib))
    (home-page "http://bio.math.berkeley.edu/eXpress")
    (synopsis "Streaming quantification for high-throughput genomic sequencing")
    (description
     "eXpress is a streaming tool for quantifying the abundances of a set of
target sequences from sampled subsequences.  Example applications include
transcript-level RNA-Seq quantification, allele-specific/haplotype expression
analysis (from RNA-Seq), transcription factor binding quantification in
ChIP-Seq, and analysis of metagenomic data.")
    (license license:artistic2.0)))

(define-public express-beta-diversity
  (package
   (name "express-beta-diversity")
   (version "1.0.8")
   (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/dparks1134/ExpressBetaDiversity")
                   (commit (string-append "v" version))))
             (file-name (git-file-name name version))
             (sha256
              (base32
               "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x"))))
   (build-system gnu-build-system)
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (delete 'configure)
        (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
        (replace 'check
          (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t))
        (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
              (install-file "../scripts/convertToEBD.py" bin)
              (install-file "../bin/ExpressBetaDiversity" bin)
              #t))))))
   (inputs
    `(("python" ,python-2)))
   (home-page "https://github.com/dparks1134/ExpressBetaDiversity")
   (synopsis "Taxon- and phylogenetic-based beta diversity measures")
   (description
    "Express Beta Diversity (EBD) calculates ecological beta diversity
(dissimilarity) measures between biological communities.  EBD implements a
variety of diversity measures including those that make use of phylogenetic
similarity of community members.")
   (license license:gpl3+)))

(define-public fanc
  (let ((commit "354401e52ba2320e6b1ba0d3b5aab3541d31c9f3")
	(revision "1"))
    (package
      (name "fanc")
      (version (git-version "0" revision commit))
      (source (origin
		(method git-fetch)
		(uri (git-reference
		      (url "https://github.com/vaquerizaslab/fanc.git")
		      (commit commit)))
		(file-name (git-file-name name version))
		(sha256
		 (base32
		  "0vp2cak5snla4j2q23d3ixx016bwzvxfiv4z6yp7anl0xaksd5bl"))))
      (build-system pyproject-build-system)
      (arguments
       (list
        #:test-flags
        '(list "-m" "not longrunning"
               ;; XXX: some of the tests here just take forever
               "--ignore=fanc/test/test_matrix.py")))
      (propagated-inputs
       (list python-biopython
	     python-cooler
             python-deprecated
	     python-future
	     python-genomic-regions
	     python-gridmap
	     python-h5py
	     python-imageio
	     python-intervaltree
	     python-matplotlib
	     python-msgpack
	     python-msgpack-numpy
             python-numpy
	     python-pandas
	     python-pillow
	     python-progressbar2
	     python-pybedtools
	     python-pybigwig
	     python-pysam
	     python-pywavelets
	     python-pyyaml
	     python-scikit-image
	     python-scikit-learn
	     python-scipy
	     python-seaborn
	     python-tables
	     python-tifffile))
      (native-inputs
       (list python-cython python-pytest))
      (home-page "https://github.com/vaquerizaslab/fanc")
      (synopsis "Framework for the analysis of C-like data")
      (description "FAN-C provides a pipeline for analysing Hi-C data starting
at mapped paired-end sequencing reads.")
      (license license:gpl3+))))

(define-public fasttree
  (package
   (name "fasttree")
   (version "2.1.10")
   (source (origin
             (method url-fetch)
             (uri (string-append
                   "http://www.microbesonline.org/fasttree/FastTree-"
                   version ".c"))
             (sha256
              (base32
               "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
   (build-system gnu-build-system)
   (arguments
    `(#:tests? #f ; no "check" target
      #:phases
      (modify-phases %standard-phases
        (delete 'unpack)
        (delete 'configure)
        (replace 'build
          (lambda* (#:key source #:allow-other-keys)
            (invoke "gcc"
                    "-O3"
                    "-finline-functions"
                    "-funroll-loops"
                    "-Wall"
                    "-o"
                    "FastTree"
                    source
                    "-lm")
            (invoke "gcc"
                    "-DOPENMP"
                    "-fopenmp"
                    "-O3"
                    "-finline-functions"
                    "-funroll-loops"
                    "-Wall"
                    "-o"
                    "FastTreeMP"
                    source
                    "-lm")
            #t))
        (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
              (install-file "FastTree" bin)
              (install-file "FastTreeMP" bin)
              #t))))))
   (home-page "http://www.microbesonline.org/fasttree")
   (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
   (description
    "FastTree can handle alignments with up to a million of sequences in a
reasonable amount of time and memory.  For large alignments, FastTree is
100-1,000 times faster than PhyML 3.0 or RAxML 7.")
   (license license:gpl2+)))

(define-public fastx-toolkit
  (package
    (name "fastx-toolkit")
    (version "0.0.14")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "https://github.com/agordon/fastx_toolkit/releases/download/"
                version "/fastx_toolkit-" version ".tar.bz2"))
              (sha256
               (base32
                "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
    (build-system gnu-build-system)
    (inputs
     (list libgtextutils))
    (native-inputs
     (list gcc-6 ;; doesn't build with later versions
           pkg-config))
    (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
    (synopsis "Tools for FASTA/FASTQ file preprocessing")
    (description
     "The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files,
containing multiple short-reads sequences.  The main processing of such
FASTA/FASTQ files is mapping the sequences to reference genomes.  However, it
is sometimes more productive to preprocess the files before mapping the
sequences to the genome---manipulating the sequences to produce better mapping
results.  The FASTX-Toolkit tools perform some of these preprocessing tasks.")
    (license license:agpl3+)))

(define-public flash
  (package
    (name "flash")
    (version "1.2.11")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/flashpage/FLASH-"
                           version ".tar.gz"))
       (sha256
        (base32
         "1b1ns9ghbcxy92xwa2a53ikqacvnyhvca0zfv0s7986xzvvscp38"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
      #:tests? #f                       ;no tests
      #:phases
      #~(modify-phases %standard-phases
          ;; No configure script
          (delete 'configure)
          ;; No install target
          (replace 'install
            (lambda _
              (install-file "flash"
                            (string-append #$output "/bin")))))))
    (inputs (list zlib))
    (home-page "http://ccb.jhu.edu/software/FLASH/")
    (synopsis "Merge paired-end nucleotide reads from NGS experiments")
    (description "FLASH (Fast Length Adjustment of SHort reads) is a tool to
merge paired-end reads from next-generation sequencing experiments.  FLASH is
designed to merge pairs of reads when the original DNA fragments are shorter
than twice the length of reads.  The resulting longer reads can significantly
improve genome assemblies.  They can also improve transcriptome assembly when
FLASH is used to merge RNA-seq data.")
    (license license:gpl3+)))

(define-public flexbar
  (package
    (name "flexbar")
    (version "3.4.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/seqan/flexbar")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2"))))
    (build-system cmake-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'do-not-tune-to-CPU
           (lambda _
             (substitute* "src/CMakeLists.txt"
               ((" -march=native") ""))))
         (replace 'check
           (lambda* (#:key outputs #:allow-other-keys)
             (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
             (with-directory-excursion "../source/test"
               (invoke "bash" "flexbar_test.sh"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (string-append (assoc-ref outputs "out")))
                    (bin (string-append out "/bin/")))
               (install-file "flexbar" bin)))))))
    (inputs
     (list tbb-2020 zlib))
    (native-inputs
     (list pkg-config seqan-2))
    (home-page "https://github.com/seqan/flexbar")
    (synopsis "Barcode and adapter removal tool for sequencing platforms")
    (description
     "Flexbar preprocesses high-throughput nucleotide sequencing data
efficiently.  It demultiplexes barcoded runs and removes adapter sequences.
Moreover, trimming and filtering features are provided.  Flexbar increases
read mapping rates and improves genome and transcriptome assemblies.  It
supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
    (license license:bsd-3)))

(define-public fxtract
  (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
    (package
      (name "fxtract")
      (version "2.3")
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/ctSkennerton/fxtract")
               (commit version)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0hab3gpwf4w9s87qlbswq6ws1qqybh4dcqk79q1ahyldzai5fgp5"))))
      (build-system gnu-build-system)
      (arguments
       `(#:make-flags ,#~(list
                          (string-append "PREFIX=" #$output)
                          "CC=gcc")
         #:test-target "fxtract_test"
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (add-before 'build 'copy-util
             (lambda* (#:key inputs #:allow-other-keys)
               (rmdir "util")
               (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
               #t))
           ;; Do not use make install as this requires additional dependencies.
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
                      (bin (string-append out"/bin")))
                 (install-file "fxtract" bin)
                 #t))))))
      (inputs
       (list pcre zlib))
      (native-inputs
       ;; ctskennerton-util is licensed under GPL2.
       `(("ctskennerton-util"
          ,(origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/ctSkennerton/util")
                   (commit util-commit)))
             (file-name (string-append
                         "ctstennerton-util-" util-commit "-checkout"))
             (sha256
              (base32
               "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
      (home-page "https://github.com/ctSkennerton/fxtract")
      (synopsis "Extract sequences from FASTA and FASTQ files")
      (description
       "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
or FASTQ) file given a subsequence.  It uses a simple substring search for
basic tasks but can change to using POSIX regular expressions, PCRE, hash
lookups or multi-pattern searching as required.  By default fxtract looks in
the sequence of each record but can also be told to look in the header,
comment or quality sections.")
      ;; 'util' requires SSE instructions.
      (supported-systems '("x86_64-linux"))
      (license license:expat))))

(define-public gemma
  (package
    (name "gemma")
    (version "0.98.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/genetics-statistics/GEMMA")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (delete-file-recursively "contrib")
                  #t))))
    (build-system gnu-build-system)
    (inputs
     (list gsl openblas zlib))
    (native-inputs
     `(("catch" ,catch2-1)
       ("perl" ,perl)
       ("shunit2" ,shunit2)
       ("which" ,which)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (add-after 'unpack 'prepare-build
           (lambda* (#:key inputs #:allow-other-keys)
             (mkdir-p "bin")
             (substitute* "Makefile"
               (("/usr/local/opt/openblas")
                (assoc-ref inputs "openblas")))
             #t))
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               ;; 'make slow-check' expects shunit2-2.0.3.
               (with-directory-excursion "test"
                 (invoke "./test_suite.sh"))
               #t)))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (install-file "bin/gemma"
                           (string-append (assoc-ref outputs "out") "/bin"))
             #t)))))
    (home-page "https://github.com/genetics-statistics/GEMMA")
    (synopsis "Tool for genome-wide efficient mixed model association")
    (description
     "@acronym{GEMMA, Genome-wide Efficient Mixed Model Association} provides a
standard linear mixed model resolver with application in @acronym{GWAS,
genome-wide association studies}.")
    (license license:gpl3)))

(define-public hisat
  (package
    (name "hisat")
    (version "0.1.6")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
                    version "-beta-source.zip"))
              (sha256
               (base32
                "177z85vqp9b30vgxl5py5hz4mm37ila37nzhfam23ci9iyfxgyv9"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no check target
       #:make-flags '("allall"
                      ;; Disable unsupported `popcnt' instructions on
                      ;; architectures other than x86_64
                      ,@(if (string-prefix? "x86_64"
                                            (or (%current-target-system)
                                                (%current-system)))
                            '()
                            '("POPCNT_CAPABILITY=0")))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-sources
           (lambda _
             ;; XXX Cannot use snippet because zip files are not supported
             (substitute* "Makefile"
               (("^CC = .*$") "CC = gcc")
               (("^CPP = .*$") "CPP = g++")
               ;; replace BUILD_HOST and BUILD_TIME for deterministic build
               (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
               (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
             (substitute* '("hisat-build" "hisat-inspect")
               (("/usr/bin/env") (which "env")))
             ;; This "extended character" is not considered valid.
             (substitute* "processor_support.h"
               (("“") "\"")
               (("”") "\""))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
               (for-each (lambda (file)
                           (install-file file bin))
                         (find-files
                          "."
                          "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))))
         (delete 'configure))))
    (native-inputs
     (list gcc-10 unzip))
    (inputs
     (list perl python zlib))
    ;; Non-portable SSE instructions are used so building fails on platforms
    ;; other than x86_64.
    (supported-systems '("x86_64-linux"))
    (home-page "https://ccb.jhu.edu/software/hisat/index.shtml")
    (synopsis "Hierarchical indexing for spliced alignment of transcripts")
    (description
     "HISAT is a fast and sensitive spliced alignment program for mapping
RNA-seq reads.  In addition to one global FM index that represents a whole
genome, HISAT uses a large set of small FM indexes that collectively cover the
whole genome.  These small indexes (called local indexes) combined with
several alignment strategies enable effective alignment of RNA-seq reads, in
particular, reads spanning multiple exons.")
    (license license:gpl3+)))

(define-public hisat2
  (package
    (name "hisat2")
    (version "2.2.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/DaehwanKimLab/hisat2/")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; no check target
       #:make-flags (list "CC=gcc" "CXX=g++" "allall")
       #:modules ((guix build gnu-build-system)
                  (guix build utils)
                  (srfi srfi-26))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'make-deterministic
           (lambda _
             (substitute* "Makefile"
               (("`date`") "0"))))
         (delete 'configure)
         (add-before 'build 'build-manual
           (lambda _
             (mkdir-p "doc")
             (invoke "make" "doc")))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin/"))
                    (doc (string-append out "/share/doc/hisat2/")))
               (for-each
                (cut install-file <> bin)
                (find-files "."
                            "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
               (mkdir-p doc)
               (install-file "doc/manual.inc.html" doc)))))))
    (native-inputs
     (list perl pandoc))             ; for documentation
    (inputs
     `(("python" ,python-wrapper)))
    (home-page "https://daehwankimlab.github.io/hisat2/")
    (synopsis "Graph-based alignment of genomic sequencing reads")
    (description "HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (both DNA and RNA) to a population of human
genomes (as well as to a single reference genome).  In addition to using one
global @dfn{graph FM} (GFM) index that represents a population of human
genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
the whole genome.  These small indexes, combined with several alignment
strategies, enable rapid and accurate alignment of sequencing reads.  This new
indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
    ;; HISAT2 contains files from Bowtie2, which is released under
    ;; GPLv2 or later.  The HISAT2 source files are released under
    ;; GPLv3 or later.
    (license license:gpl3+)))

(define-public homer
  (package
    (name "homer")
    (version "4.11.1")
    (source
     (origin
       (method url-fetch/zipbomb)
       (uri (string-append "http://homer.ucsd.edu/homer/data/software/homer.v"
                           version ".zip"))
       (sha256
        (base32
         "0ay802swzq6ix9d8fkinpplcvyc1xyi3cjmj2x08jab7c40cvlc0"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (replace 'configure
            (lambda _
              (let ((share (string-append #$output "/share/homer")))
                (mkdir-p share)
                (substitute* "configureHomer.pl"
                  (("my \\$homeDir = \\$1;")
                   (string-append "my $homeDir = \"" share "\";"))))))
          (replace 'build
            (lambda _
              (let ((share (string-append #$output "/share/homer")))
                (copy-recursively "." share))
              (invoke "perl" "configureHomer.pl" "-local")))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (invoke (string-append #$output "/share/homer/bin/homer2")))))
          (replace 'install
            (lambda _
              (mkdir-p (string-append #$output "/bin"))
              (symlink (string-append #$output "/share/homer/bin/homer2")
                       (string-append #$output "/bin/homer2"))
              (for-each patch-shebang
                        (find-files (string-append #$output "/share/homer/bin")
                                    "\\.pl$")))))))
    (inputs
     (list perl))
    (native-inputs
     (list perl unzip))
    (home-page "http://homer.ucsd.edu/homer")
    (synopsis "Motif discovery and next generation sequencing analysis")
    (description
     "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of
tools for Motif Discovery and next-gen sequencing analysis.  It is a
collection of command line programs written in Perl and C++.  HOMER was
primarily written as a de novo motif discovery algorithm and is well suited
for finding 8-20 bp motifs in large scale genomics data.  HOMER contains many
useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and
numerous other types of functional genomics sequencing data sets.")
    (license license:gpl3+)))

(define-public hmmer
  (package
    (name "hmmer")
    (version "3.3.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz"))
       (sha256
        (base32
         "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj"))))
    (build-system gnu-build-system)
    (native-inputs (list perl python)) ; for tests
    (home-page "http://hmmer.org/")
    (synopsis "Biosequence analysis using profile hidden Markov models")
    (description
     "HMMER is used for searching sequence databases for homologs of protein
sequences, and for making protein sequence alignments.  It implements methods
using probabilistic models called profile hidden Markov models (profile
HMMs).")
    ;; hmmer uses non-portable SSE intrinsics so building fails on other
    ;; platforms.
    (supported-systems '("x86_64-linux" "i686-linux"))
    (license license:bsd-3)))

(define-public htseq
  (package
    (name "htseq")
    (version "2.0.2")
    ;; Sources on pypi do not include everything needed to run the tests.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/htseq/htseq")
                    (commit (string-append "release_" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19"))))
    (build-system python-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         ;; Avoid rebuilding the extension.  Everything is built during the
         ;; 'install phase anyway.
         (delete 'build)
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "pytest" "-v")))))))
    (propagated-inputs
     (list python-matplotlib
           python-numpy
           python-pysam))
    (native-inputs
     (list python-cython
           python-pandas
           python-pytest
           python-scipy
           swig))
    (home-page "https://github.com/htseq")
    (synopsis "Framework for analyzing high-throughput sequencing data")
    (description
     "This package provides a framework to process and analyze data from
high-throughput sequencing (HTS) assays")
    (license license:gpl3+)))

(define-public python-genomepy
  (package
    (name "python-genomepy")
    (version "0.15.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "genomepy" version))
              (sha256
               (base32
                "0jmyvnsn6w0djjmxh4fjspy1346337jzihxb276v3s275r6zjmln"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      ;; The tests require internet access.
      #:tests? #false
      #:phases
      '(modify-phases %standard-phases
         ;; Needed by tests
         (add-after 'unpack 'set-HOME
           (lambda _ (setenv "HOME" "/tmp"))))))
    (propagated-inputs (list python-appdirs
                             python-biopython
                             python-click
                             python-colorama
                             python-diskcache
                             ;; We cannot use an older filelock, because the
                             ;; @lock annotation is used here.
                             python-filelock-3.5
                             python-loguru
                             python-mygene
                             python-mysql-connector-python
                             python-norns
                             python-numpy
                             python-pandas
                             python-pyfaidx
                             python-requests
                             python-tqdm))
    (native-inputs (list python-hatchling python-pytest))
    (home-page "https://vanheeringen-lab.github.io/genomepy/")
    (synopsis "Genes and genomes at your fingertips")
    (description "genomepy is designed to provide a simple and straightforward
way to download and use genomic data.  This includes

@enumerate
@item searching available data,
@item showing the available metadata,
@item automatically downloading, preprocessing and matching data, and
@item generating optional aligner indexes.
@end enumerate

All with sensible, yet controllable defaults.")
    (license license:expat)))

(define-public java-htsjdk
  (package
    (name "java-htsjdk")
    (version "2.3.0") ; last version without build dependency on gradle
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/samtools/htsjdk")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1b178ixcabanm834ydjl3jiakpyxdmki32hqfv2abrzn3rcwa28i"))
              (modules '((guix build utils)))
              (snippet
               ;; Delete pre-built binaries
               '(begin
                  (delete-file-recursively "lib")
                  (mkdir-p "lib")
                  #t))))
    (build-system ant-build-system)
    (arguments
     `(#:tests? #f ; test require Internet access
       #:jdk ,icedtea-8
       #:make-flags
       ,#~(list (string-append "-Ddist=" #$output "/share/java/htsjdk/"))
       #:build-target "all"
       #:phases
       (modify-phases %standard-phases
         ;; The build phase also installs the jars
         (delete 'install))))
    (inputs
     `(("java-ngs" ,java-ngs)
       ("java-snappy-1" ,java-snappy-1)
       ("java-commons-compress" ,java-commons-compress)
       ("java-commons-logging-minimal" ,java-commons-logging-minimal)
       ("java-commons-jexl-2" ,java-commons-jexl-2)
       ("java-xz" ,java-xz)))
    (native-inputs
     (list java-testng))
    (home-page "https://samtools.github.io/htsjdk/")
    (synopsis "Java API for high-throughput sequencing data (HTS) formats")
    (description
     "HTSJDK is an implementation of a unified Java library for accessing
common file formats, such as SAM and VCF, used for high-throughput
sequencing (HTS) data.  There are also an number of useful utilities for
manipulating HTS data.")
    (license license:expat)))

(define-public java-htsjdk-latest
  (package
    (name "java-htsjdk")
    (version "2.14.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/samtools/htsjdk")
                    (commit version)))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
    (build-system ant-build-system)
    (arguments
     `(#:tests? #f                      ; test require Scala
       #:jdk ,icedtea-8
       #:jar-name "htsjdk.jar"
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'remove-useless-build.xml
           (lambda _ (delete-file "build.xml") #t))
         ;; The tests require the scalatest package.
         (add-after 'unpack 'remove-tests
           (lambda _ (delete-file-recursively "src/test") #t)))))
    (inputs
     `(("java-ngs" ,java-ngs)
       ("java-snappy-1" ,java-snappy-1)
       ("java-commons-compress" ,java-commons-compress)
       ("java-commons-logging-minimal" ,java-commons-logging-minimal)
       ("java-commons-jexl-2" ,java-commons-jexl-2)
       ("java-xz" ,java-xz)))
    (native-inputs
     (list java-junit))
    (home-page "https://samtools.github.io/htsjdk/")
    (synopsis "Java API for high-throughput sequencing data (HTS) formats")
    (description
     "HTSJDK is an implementation of a unified Java library for accessing
common file formats, such as SAM and VCF, used for high-throughput
sequencing (HTS) data.  There are also an number of useful utilities for
manipulating HTS data.")
    (license license:expat)))

;; This is needed for picard 2.10.3
(define-public java-htsjdk-2.10.1
  (package (inherit java-htsjdk-latest)
    (name "java-htsjdk")
    (version "2.10.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/samtools/htsjdk")
                    (commit version)))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2"))))
    (build-system ant-build-system)
    (arguments
     `(#:tests? #f                      ; tests require Scala
       #:jdk ,icedtea-8
       #:jar-name "htsjdk.jar"
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'remove-useless-build.xml
           (lambda _ (delete-file "build.xml") #t))
         ;; The tests require the scalatest package.
         (add-after 'unpack 'remove-tests
           (lambda _ (delete-file-recursively "src/test") #t)))))))

(define-public java-maxent
  (package
    (name "java-maxent")
    (version "3.4.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/mrmaxent/Maxent")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "12q7hhly76l77vm8w8v9icga2gn6xs0bw33a7wb7zikcmvizcyp0"))))
    (build-system ant-build-system)
    (arguments
     (list
      #:tests? #false                   ;there are none
      #:jdk icedtea-8
      #:phases
      #~(modify-phases %standard-phases
          (replace 'build
            (lambda* (#:key inputs #:allow-other-keys)
              ;; See https://github.com/mrmaxent/Maxent/pull/11
              (substitute* "density/Extractor.java"
                (("float") "double"))
              (with-directory-excursion "gnu/getopt/"
                (invoke "make"))
              (mkdir-p "ptii")
              (with-directory-excursion "ptii"
                (invoke "tar" "xvf" (assoc-ref inputs "ptii")
                        "--strip-components=1")
                (copy-recursively "com" "../com"))
              (delete-file-recursively "ptii")
              (apply invoke "javac" "-cp" (getcwd) "-g"
                     (find-files "com/microstar/xml" "\\.java$"))
              (apply invoke "javac" "-cp" (getcwd) "-g"
                     (find-files "density" "\\.java$"))

              ;; This needs the proprietary com.sun.image.codec.jpeg module.
              (delete-file "ptolemy/plot/servlet/PlotServlet.java")
              (apply invoke "javac" "-cp"
                     (string-append (getcwd) ":" (getenv "CLASSPATH")) "-g"
                     (find-files "ptolemy/plot" "\\.java$"))
              (apply invoke "javac" "-cp" (getcwd) "-g"
                     (find-files "com" "\\.java$"))
              (apply invoke "javac" "-cp" (getcwd) "-g"
                     (find-files "gui" "\\.java$"))
              (apply invoke "jar" "cvfm" "maxent.jar"
                     (cons* "density/mc.mf"
                            "density/parameters.csv"
                            (append (find-files "density" "\\.class$")
                                    (find-files "density" "\\.html$")
                                    (find-files "gnu/getopt" ".*")
                                    (find-files "gui/layouts" "\\.class$")
                                    (find-files "com/macfaq/io" "\\.class$")
                                    (find-files "density/tools" "\\.class$")
                                    (find-files "ptolemy/plot" "\\.class$"))))))
          (replace 'install
            (lambda _
              (install-file "maxent.jar"
                            (string-append #$output "/share/java/maxent/")))))))
    (inputs
     (list java-classpathx-servletapi))
    (native-inputs
     `(("make" ,gnu-make)
       ;; For com.microstar.xml
       ("ptii"
        ,(let ((version "4.0.1"))
           (origin
             (method url-fetch)
             (uri (string-append "https://ptolemy.berkeley.edu/ptolemyII/ptII"
                                 (version-major+minor version)
                                 "/ptII" version ".src.tar.gz"))
             (sha256
              (base32
               "0ifmmvrcipcnd4b9im1g379ffrs7g7k99sw5vv9d9h3hzq6hqv21")))))))
    (home-page "http://biodiversityinformatics.amnh.org/open_source/maxent")
    (synopsis "Model species geographic distributions")
    (description
     "Maxent is a stand-alone Java application for modelling species
geographic distributions.")
    (license license:expat)))

;; This version matches java-htsjdk 2.3.0.  Later versions also require a more
;; recent version of java-htsjdk, which depends on gradle.
(define-public java-picard
  (package
    (name "java-picard")
    (version "2.3.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/broadinstitute/picard")
                    (commit version)))
              (file-name (string-append "java-picard-" version "-checkout"))
              (sha256
               (base32
                "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Delete pre-built binaries.
                  (delete-file-recursively "lib")
                  (mkdir-p "lib")
                  (substitute* "build.xml"
                    ;; Remove build-time dependency on git.
                    (("failifexecutionfails=\"true\"")
                     "failifexecutionfails=\"false\"")
                    ;; Use our htsjdk.
                    (("depends=\"compile-htsjdk, ")
                     "depends=\"")
                    (("depends=\"compile-htsjdk-tests, ")
                     "depends=\"")
                    ;; Build picard-lib.jar before building picard.jar
                    (("name=\"picard-jar\" depends=\"" line)
                     (string-append line "picard-lib-jar, ")))
                  #t))))
    (build-system ant-build-system)
    (arguments
     `(#:build-target "picard-jar"
       #:test-target "test"
       ;; Tests require jacoco:coverage.
       #:tests? #f
       #:make-flags
       ,#~(list (string-append "-Dhtsjdk_lib_dir="
                               #$(this-package-input "java-htsjdk")
                               "/share/java/htsjdk/")
                "-Dhtsjdk-classes=dist/tmp"
                (string-append "-Dhtsjdk-version="
                               #$(package-version java-htsjdk)))
       #:jdk ,icedtea-8
       #:phases
       (modify-phases %standard-phases
         ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class"
         (delete 'generate-jar-indices)
         (add-after 'unpack 'fix-guava
           (lambda _
             (substitute* "src/java/picard/cmdline/CommandLineParser.java"
               (("CharMatcher.ASCII") "CharMatcher.ascii()"))))
         (add-after 'unpack 'use-our-htsjdk
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "build.xml"
               (("\\$\\{htsjdk\\}/lib")
                (search-input-directory inputs
                                        "share/java/htsjdk")))))
         (add-after 'unpack 'make-test-target-independent
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "build.xml"
               (("name=\"test\" depends=\"compile, ")
                "name=\"test\" depends=\""))
             #t))
         (replace 'install (install-jars "dist")))))
    (inputs
     (list java-htsjdk java-guava))
    (native-inputs
     (list java-testng))
    (home-page "https://broadinstitute.github.io/picard/")
    (synopsis "Tools for manipulating high-throughput sequencing data and formats")
    (description "Picard is a set of Java command line tools for manipulating
high-throughput sequencing (HTS) data and formats.  Picard is implemented
using the HTSJDK Java library to support accessing file formats that are
commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
VCF.")
    (license license:expat)))

;; This is needed for dropseq-tools
(define-public java-picard-2.10.3
  (package
    (name "java-picard")
    (version "2.10.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/broadinstitute/picard")
                    (commit version)))
              (file-name (string-append "java-picard-" version "-checkout"))
              (sha256
               (base32
                "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
    (build-system ant-build-system)
    (arguments
     `(#:jar-name "picard.jar"
       ;; Tests require jacoco:coverage.
       #:tests? #f
       #:jdk ,icedtea-8
       #:main-class "picard.cmdline.PicardCommandLine"
       #:modules ((guix build ant-build-system)
                  (guix build utils)
                  (guix build java-utils)
                  (sxml simple)
                  (sxml transform)
                  (sxml xpath))
       #:phases
       (modify-phases %standard-phases
         ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class"
         (delete 'generate-jar-indices)
         (add-after 'unpack 'remove-useless-build.xml
           (lambda _ (delete-file "build.xml") #t))
         (add-after 'unpack 'fix-guava
           (lambda _
             (substitute* "src/main/java/picard/cmdline/CommandLineParser.java"
               (("CharMatcher.ASCII") "CharMatcher.ascii()"))))
         ;; This is necessary to ensure that htsjdk is found when using
         ;; picard.jar as an executable.
         (add-before 'build 'edit-classpath-in-manifest
           (lambda* (#:key inputs #:allow-other-keys)
             (chmod "build.xml" #o664)
             (call-with-output-file "build.xml.new"
               (lambda (port)
                 (sxml->xml
                  (pre-post-order
                   (with-input-from-file "build.xml"
                     (lambda _ (xml->sxml #:trim-whitespace? #t)))
                   `((target    . ,(lambda (tag . kids)
                                     (let ((name ((sxpath '(name *text*))
                                                  (car kids)))
                                           ;; FIXME: We're breaking the line
                                           ;; early with a dummy path to
                                           ;; ensure that the store reference
                                           ;; isn't broken apart and can still
                                           ;; be found by the reference
                                           ;; scanner.
                                           (msg (format #f
                                                        "\
Class-Path: /~a \
 ~a/share/java/htsjdk.jar${line.separator}${line.separator}"
                                                        ;; maximum line length is 70
                                                        (string-tabulate (const #\b) 57)
                                                        (assoc-ref inputs "java-htsjdk"))))
                                       (if (member "manifest" name)
                                           `(,tag ,@kids
                                                  (replaceregexp
                                                   (@ (file "${manifest.file}")
                                                      (match "\\r\\n\\r\\n")
                                                      (replace "${line.separator}")))
                                                  (echo
                                                   (@ (message ,msg)
                                                      (file "${manifest.file}")
                                                      (append "true"))))
                                           `(,tag ,@kids)))))
                     (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
                     (*text*    . ,(lambda (_ txt) txt))))
                  port)))
             (rename-file "build.xml.new" "build.xml")
             #t)))))
    (propagated-inputs
     (list java-htsjdk-2.10.1))
    (native-inputs
     (list java-testng java-guava))
    (home-page "https://broadinstitute.github.io/picard/")
    (synopsis "Tools for manipulating high-throughput sequencing data and formats")
    (description "Picard is a set of Java command line tools for manipulating
high-throughput sequencing (HTS) data and formats.  Picard is implemented
using the HTSJDK Java library to support accessing file formats that are
commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
VCF.")
    (license license:expat)))

;; This is the last version of Picard to provide net.sf.samtools
(define-public java-picard-1.113
  (package (inherit java-picard)
    (name "java-picard")
    (version "1.113")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/broadinstitute/picard")
                    (commit version)))
              (file-name (string-append "java-picard-" version "-checkout"))
              (sha256
               (base32
                "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Delete pre-built binaries.
                  (delete-file-recursively "lib")
                  (mkdir-p "lib")))))
    (build-system ant-build-system)
    (arguments
     `(#:build-target "picard-jar"
       #:test-target "test"
       ;; FIXME: the class path at test time is wrong.
       ;; [testng] Error: A JNI error has occurred, please check your installation and try again
       ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
       #:tests? #f
       #:jdk ,icedtea-8
       #:ant ,ant/java8
       ;; This is only used for tests.
       #:make-flags
       (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
       #:phases
       (modify-phases %standard-phases
         ;; FIXME: This phase fails.
         (delete 'generate-jar-indices)
         ;; Do not use bundled ant bzip2.
         (add-after 'unpack 'use-ant-bzip
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "build.xml"
               (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
                (search-input-file inputs "/lib/ant.jar")))))
         (add-after 'unpack 'make-test-target-independent
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "build.xml"
               (("name=\"test\" depends=\"compile, ")
                "name=\"test\" depends=\"compile-tests, ")
               (("name=\"compile\" depends=\"compile-src, compile-tests\"")
                "name=\"compile\" depends=\"compile-src\""))))
         (add-after 'unpack 'fix-deflater-path
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "src/java/net/sf/samtools/Defaults.java"
               (("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
                (string-append "getStringProperty(\"intel_deflater_so_path\", \""
                               (assoc-ref outputs "out")
                               "/lib/jni/libIntelDeflater.so"
                               "\")")))))
         ;; Build the deflater library, because we've previously deleted the
         ;; pre-built one.  This can only be built with access to the JDK
         ;; sources.
         (add-after 'build 'build-jni
           (lambda* (#:key inputs #:allow-other-keys)
             (mkdir-p "lib/jni")
             (mkdir-p "jdk-src")
             (invoke "tar" "--strip-components=1" "-C" "jdk-src"
                     "-xf" (assoc-ref inputs "jdk-src"))
             (invoke "javah" "-jni"
                     "-classpath" "classes"
                     "-d" "lib/"
                     "net.sf.samtools.util.zip.IntelDeflater")
             (with-directory-excursion "src/c/inteldeflater"
               (invoke "gcc" "-I../../../lib" "-I."
                       (string-append "-I" (assoc-ref inputs "jdk")
                                      "/include/linux")
                       "-I../../../jdk-src/src/share/native/common/"
                       "-I../../../jdk-src/src/solaris/native/common/"
                       "-c" "-O3" "-fPIC" "IntelDeflater.c")
               (invoke "gcc" "-shared"
                       "-o" "../../../lib/jni/libIntelDeflater.so"
                       "IntelDeflater.o" "-lz" "-lstdc++"))))
         ;; We can only build everything else after building the JNI library.
         (add-after 'build-jni 'build-rest
           (lambda* (#:key make-flags #:allow-other-keys)
             (apply invoke `("ant" "all" ,@make-flags))))
         (add-before 'build 'set-JAVA6_HOME
           (lambda _
             (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))))
         (replace 'install (install-jars "dist"))
         (add-after 'install 'install-jni-lib
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((jni (string-append (assoc-ref outputs "out")
                                       "/lib/jni")))
               (mkdir-p jni)
               (install-file "lib/jni/libIntelDeflater.so" jni)))))))
    (inputs
     (list java-snappy-1
           java-commons-jexl-2
           java-cofoja
           ant/java8                    ;for bzip2 support at runtime
           zlib))
    (native-inputs
     `(("ant-apache-bcel" ,ant-apache-bcel)
       ("ant-junit" ,ant-junit)
       ("java-testng" ,java-testng)
       ("java-commons-bcel" ,java-commons-bcel)
       ("java-jcommander" ,java-jcommander)
       ("jdk" ,icedtea-8 "jdk")
       ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))

(define-public fastqc
  (package
    (name "fastqc")
    (version "0.11.9")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/s-andrews/FastQC")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "00y9drm0bkpxw8xfl8ysss18jmnhj8blgqgr6fpa58rkpfcbg8qk"))
       (snippet
        '(for-each delete-file
                   '("cisd-jhdf5.jar"
                     "sam-1.103.jar"
                     "jbzip2-0.9.jar")))))
    (build-system ant-build-system)
    (arguments
     (list
      #:tests? #f                       ;there are no tests
      #:build-target "build"
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-dependencies
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* '("build.xml" ".classpath")
                (("jbzip2-0.9.jar")
                 (search-input-file inputs "/share/java/jbzip2.jar"))
                (("sam-1.103.jar")
                 (search-input-file inputs "/share/java/sam-1.112.jar"))
                (("cisd-jhdf5.jar")
                 (search-input-file inputs "/share/java/sis-jhdf5.jar")))))
          ;; There is no installation target
          (replace 'install
            (lambda* (#:key inputs #:allow-other-keys)
              (let* ((bin   (string-append #$output "/bin"))
                     (share (string-append #$output "/share/fastqc/"))
                     (exe   (string-append share "/fastqc")))
                (for-each mkdir-p (list bin share))
                (copy-recursively "bin" share)
                (substitute* exe
                  (("my \\$java_bin = \"java\";")
                   (string-append "my $java_bin = \""
                                  ;; Use java from the JRE, not the JDK
                                  #$(this-package-input "icedtea") "/bin/java"
                                  "\";"))
                  (("\\$RealBin\\$delimiter\\$RealBin.*")
                   (string-append
                    (string-join
                     (list
                      share
                      (search-input-file inputs "/share/java/sam-1.112.jar")
                      (search-input-file inputs "/share/java/jbzip2.jar")
                      (search-input-file inputs "/share/java/sis-jhdf5.jar"))
                     "$delimiter")
                    "\";\n")))
                (chmod exe #o555)
                (symlink exe (string-append bin "/fastqc"))))))))
    (inputs
     (list icedtea
           java-cisd-jhdf5
           java-picard-1.113
           java-jbzip2
           perl))                       ;needed for the wrapper script
    (native-inputs
     (list unzip))
    (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
    (synopsis "Quality control tool for high throughput sequence data")
    (description
     "FastQC aims to provide a simple way to do some quality control
checks on raw sequence data coming from high throughput sequencing
pipelines.  It provides a modular set of analyses which you can use to
give a quick impression of whether your data has any problems of which
you should be aware before doing any further analysis.

The main functions of FastQC are:

@itemize
@item Import of data from BAM, SAM or FastQ files (any variant);
@item Providing a quick overview to tell you in which areas there may
  be problems;
@item Summary graphs and tables to quickly assess your data;
@item Export of results to an HTML based permanent report;
@item Offline operation to allow automated generation of reports
  without running the interactive application.
@end itemize\n")
    (license license:gpl3+)))

(define-public fastp
  (package
    (name "fastp")
    (version "0.23.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/OpenGene/fastp")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "04nmrqpjc3qni0cbazlwvpg8rk1mkfmfma0n4q3zivs3zi6rfnav"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #false                   ;there are none
      #:make-flags
      #~(list (string-append "PREFIX=" #$output))
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (add-before 'install 'create-target-dir
            (lambda _
              (mkdir-p (string-append #$output "/bin")))))))
    (inputs
     (list isa-l libdeflate))
    (home-page "https://github.com/OpenGene/fastp/")
    (synopsis "All-in-one FastQ preprocessor")
    (description
     "Fastp is a tool designed to provide fast all-in-one preprocessing for
FastQ files.  This tool has multi-threading support to afford high
performance.")
    (license license:expat)))

(define-public htscodecs
  (package
    (name "htscodecs")
    (version "1.6.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/samtools/htscodecs/"
                                  "releases/download/v"
                                  version "/htscodecs-" version ".tar.gz"))
              (sha256
               (base32
                "1h0827g9svil9jnjbpdlxjbl44rai5b95m61hs9ifbqrz9nvnjjb"))))
    (build-system gnu-build-system)
    (inputs (list bzip2 zlib))
    (home-page "https://github.com/samtools/htscodecs")
    (synopsis "Custom compression for CRAM and others")
    (description
     "This package implements the custom CRAM codecs used for \"EXTERNAL\"
block types.  These consist of two variants of the rANS codec (8-bit and
16-bit renormalisation, with run-length encoding and bit-packing also
supported in the latter), a dynamic arithmetic coder, and custom codecs for
name/ID compression and quality score compression derived from fqzcomp.")
    (license
     (list license:public-domain ;c_range_coder.h, rANS_byte.h, and rANS_word.h
           license:bsd-3))))     ;all the rest

(define-public htslib
  (package
    (name "htslib")
    (version "1.19")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "0dh79lwpspwwfbkmllrrhbk8nkvlfc5b5ib4d0xg5ld79w6c8lc7"))
              (snippet
               #~(begin
                   (use-modules (guix build utils))
                   (delete-file-recursively "htscodecs")))))
    (build-system gnu-build-system)
    ;; Let htslib translate "gs://" and "s3://" to regular https links with
    ;; "--enable-gcs" and "--enable-s3". For these options to work, we also
    ;; need to set "--enable-libcurl".
    (arguments
     `(#:configure-flags '("--enable-gcs"
                           "--enable-libcurl"
                           "--enable-s3"
                           "--with-external-htscodecs")))
    (inputs
     (list bzip2 curl openssl xz))
    ;; This is referred to in the pkg-config file as a required library.
    (propagated-inputs
     (list htscodecs zlib))
    (native-inputs
     (list perl))
    (home-page "https://www.htslib.org")
    (synopsis "C library for reading/writing high-throughput sequencing data")
    (description
     "HTSlib is a C library for reading/writing high-throughput sequencing
data.  It also provides the @command{bgzip}, @command{htsfile}, and
@command{tabix} utilities.")
    ;; Files under cram/ are released under the modified BSD license;
    ;; the rest is released under the Expat license
    (license (list license:expat license:bsd-3))))

(define-public htslib-1.14
  (package/inherit htslib
    (version "1.14")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd"))))
    (arguments
     (substitute-keyword-arguments (package-arguments htslib)
       ((#:configure-flags cf #~'())
        #~(delete "--with-external-htscodecs" #$cf))))
    (propagated-inputs
     (modify-inputs (package-propagated-inputs htslib)
                    (delete "htscodecs")))))

(define-public htslib-1.12
  (package/inherit htslib
    (version "1.12")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012"))))
    (arguments
     (substitute-keyword-arguments (package-arguments htslib)
       ((#:configure-flags cf #~'())
        #~(delete "--with-external-htscodecs" #$cf))))
    (propagated-inputs
     (modify-inputs (package-propagated-inputs htslib)
                    (delete "htscodecs")))))

(define-public htslib-1.10
  (package/inherit htslib
    (version "1.10")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "0wm9ay7qgypj3mwx9zl1mrpnr36298b1aj5vx69l4k7bzbclvr3s"))))))

(define-public htslib-1.9
  (package/inherit htslib
    (version "1.9")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))))

;; This package should be removed once no packages rely upon it.
(define htslib-1.3
  (package/inherit htslib
    (version "1.3.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))

(define htslib-for-samtools-1.2
  (package/inherit htslib
    (version "1.2.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx"))))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-tests
           (lambda _
             (substitute* "test/test.pl"
               (("/bin/bash") (which "bash"))))))))
    (inputs
     `(("zlib" ,zlib)))
    (native-inputs
     `(("perl" ,perl)))))

(define htslib-for-stringtie
  (package
    (inherit htslib-1.12)
    (source (origin
              (inherit (package-source htslib-1.12))
              (patches
               (search-patches "htslib-for-stringtie.patch"))))
    (arguments
     `(#:configure-flags '("--with-libdeflate")))
    (inputs
     (list bzip2 libdeflate openssl))))

(define-public idr
  (package
    (name "idr")
    (version "2.0.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/nboley/idr")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "04j876h6z444v2q79drxx283d3k5snd72kj895wbalnl42206x9g"))
              ;; Delete generated C code.
              (snippet
               '(begin (delete-file "idr/inv_cdf.c") #t))))
    (build-system python-build-system)
    ;; There is only one test ("test_inv_cdf.py") and it tests features that
    ;; are no longer part of this package.  It also asserts False, which
    ;; causes the tests to always fail.
    (arguments `(#:tests? #f))
    (propagated-inputs
     (list python-scipy python-sympy python-numpy python-matplotlib))
    (native-inputs
     (list python-cython))
    (home-page "https://github.com/nboley/idr")
    (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
    (description
     "The IDR (Irreproducible Discovery Rate) framework is a unified approach
to measure the reproducibility of findings identified from replicate
experiments and provide highly stable thresholds based on reproducibility.")
    (license license:gpl2+)))

(define-public isolator
  (let ((commit "24bafc0a102dce213bfc2b5b9744136ceadaba03")
        (revision "1"))
    (package
      (name "isolator")
      (version (git-version "0.0.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/dcjones/isolator.git")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "12mbcfqhiggcjvzizf2ff7b05z31i47njcyzcivpw5j74pfbr3dv"))))
      (build-system cmake-build-system)
      (arguments
       (list
        #:tests? #f                     ;no check target
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'fix-std
             (lambda _
               (substitute* '("src/summarize.cpp"
                              "src/shredder.cpp")
                 (("isnan") "std::isnan")
                 (("isinf") "std::isinf")))))))
      (inputs
       (list boost hdf5 zlib))
      (home-page "https://github.com/dcjones/isolator")
      (synopsis "Tools for the analysis of RNA-Seq experiments")
      (description "Isolator analyzes RNA-Seq experiments.  Isolator has a
particular focus on producing stable, consistent estimates.  It implements a
full hierarchical Bayesian model of an entire RNA-Seq experiment.  It saves
all the samples generated by the sampler, which can be processed to compute
posterior probabilities for arbitrarily complex questions, far beyond the
confines of pairwise tests.  It aggressively corrects for technical effects,
such as random priming bias, GC-bias, 3' bias, and fragmentation effects.
Compared to other MCMC approaches, it is exceedingly efficient, though
generally slower than modern maximum likelihood approaches.")
      (license license:expat))))

(define-public jellyfish
  (package
    (name "jellyfish")
    (version "2.3.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/gmarcais/Jellyfish/"
                                  "releases/download/v" version
                                  "/jellyfish-" version ".tar.gz"))
              (sha256
               (base32
                "0npa62wzasdibas5zp3n8j3armsci4kyvh0jw7jr0am4gg7vg5g1"))))
    (build-system gnu-build-system)
    (outputs '("out"      ;for library
               "python")) ;for Python bindings
    (arguments
     (list
      #:configure-flags
      #~(list "--without-sse" ; configure script probes for CPU features when SSE is enabled.
              (string-append "--enable-python-binding=" #$output:python))
      #:phases
      '(modify-phases %standard-phases
         (add-before 'check 'set-SHELL-variable
           (lambda _
             ;; generator_manager.hpp either uses /bin/sh or $SHELL
             ;; to run tests.
             (setenv "SHELL" (which "bash")))))))
    (native-inputs
     (list bc
           time
           python-wrapper
           pkg-config))
    (inputs
     (list htslib))
    (synopsis "Tool for fast counting of k-mers in DNA")
    (description
     "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
DNA.  A k-mer is a substring of length k, and counting the occurrences of all
such substrings is a central step in many analyses of DNA sequence.  Jellyfish
is a command-line program that reads FASTA and multi-FASTA files containing
DNA sequences.  It outputs its k-mer counts in a binary format, which can be
translated into a human-readable text format using the @code{jellyfish dump}
command, or queried for specific k-mers with @code{jellyfish query}.")
    (home-page "http://www.genome.umd.edu/jellyfish.html")
    ;; JELLYFISH seems to be 64-bit only.
    (supported-systems %64bit-supported-systems)
    ;; One of these licenses may be picked
    (license (list license:gpl3+ license:bsd-3))))

(define-public khmer
  (package
    (name "khmer")
    (version "3.0.0a3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/dib-lab/khmer")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "01l4jczglkl7yfhgvzx8j0df7k54bk1r8sli9ll16i1mis0d8f37"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; Delete bundled libraries.  We do not replace the bundled seqan
           ;; as it is a modified subset of the old version 1.4.1.
           ;;
           ;; We do not replace the bundled MurmurHash as the canonical
           ;; repository for this code 'SMHasher' is unsuitable for providing
           ;; a library.  See
           ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
           (delete-file-recursively "third-party/zlib")
           (delete-file-recursively "third-party/bzip2")
           (delete-file-recursively "third-party/seqan")
           (substitute* "setup.cfg"
             (("# libraries = z,bz2")
              "libraries = z,bz2")
             (("include:third-party/zlib:third-party/bzip2")
              "include:"))
           ;; Delete generated Cython CPP files.
           (for-each delete-file (find-files "khmer/_oxli/" "\\.cpp$"))))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'set-cc
           (lambda _ (setenv "CC" "gcc")))
         (add-after 'unpack 'python-3.8-compatibility
           (lambda _
             ;; Python 3.8 removed time.clock().
             (substitute* "sandbox/sweep-reads.py"
               (("time\\.clock")
                "time.process_time"))))
         (add-after 'unpack 'do-use-cython
           (lambda _
             (substitute* "setup.py"
               (("from setuptools import Extension as CyExtension")
                "from Cython.Distutils import Extension as CyExtension")
               (("from setuptools.command.build_ext import build_ext as _build_ext")
                "from Cython.Distutils import build_ext as _build_ext")
               (("HAS_CYTHON = False") "HAS_CYTHON = True")
               (("cy_ext = 'cpp'") "cy_ext = 'pyx'"))))
         (add-before 'build 'build-extensions
           (lambda _
             ;; Cython extensions have to be built before running the tests.
             (invoke "python" "setup.py" "build_ext" "--inplace")))
         (replace 'check
           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (invoke "pytest" "-v")))))))
    (native-inputs
     (list python-cython python-pytest python-pytest-runner))
    (inputs
     (list zlib bzip2 seqan-1 python-screed python-bz2file))
    (home-page "https://khmer.readthedocs.org/")
    (synopsis "K-mer counting, filtering and graph traversal library")
    (description "The khmer software is a set of command-line tools for
working with DNA shotgun sequencing data from genomes, transcriptomes,
metagenomes and single cells.  Khmer can make de novo assemblies faster, and
sometimes better.  Khmer can also identify and fix problems with shotgun
data.")
    ;; When building on i686, armhf and mips64el, we get the following error:
    ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
    (supported-systems '("x86_64-linux" "aarch64-linux"))
    (license license:bsd-3)))

(define-public kaiju
  (package
    (name "kaiju")
    (version "1.9.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/bioinformatics-centre/kaiju")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1hfmadkfs6jjd7l3byly5xxb0ifm3dm1wis11sjbqfcv6l89snmg"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ; There are no tests.
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (add-before 'build 'move-to-src-dir
            (lambda _ (chdir "src")))
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin")))
                (mkdir-p bin)
                (copy-recursively "../bin" bin)
                (let ((path (search-path-as-list '("bin")
                                                 '#$(match (package-inputs this-package)
                                                      (((_ pkg) ...) pkg)))))
                  (for-each (lambda (script)
                              (let ((exe (string-append bin "/" script)))
                                (chmod exe #o555)
                                (wrap-script exe
                                  #:guile #$(file-append guile-3.0 "/bin/guile")
                                  `("PATH" ":" prefix ,path))))
                            (list "kaiju-convertMAR.py"
                                  "kaiju-gbk2faa.pl"
                                  "kaiju-makedb")))))))))
    (inputs
     (list bzip2
           coreutils
           curl
           gawk
           guile-3.0 ;for wrap-script
           gzip
           perl
           python-wrapper
           tar
           wget
           zlib))
    (home-page "https://kaiju.binf.ku.dk/")
    (synopsis "Fast and sensitive taxonomic classification for metagenomics")
    (description "Kaiju is a program for sensitive taxonomic classification
of high-throughput sequencing reads from metagenomic whole genome sequencing
experiments.")
    (license license:gpl3+)))

(define-public macs
  (package
    (name "macs")
    (version "2.2.9.1")
    (source (origin
              ;; The PyPi tarball does not contain tests.
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/macs3-project/MACS")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "10vwc09fq4nvbd39hax1949mvq2wvkgz0k3p2zqmqwq8hv9r5l0j"))
        (modules '((guix build utils)))
        ;; Remove files generated by Cython
        (snippet
         '(begin
            (for-each (lambda (file)
                        (let ((generated-file
                                (string-append (string-drop-right file 3) "c")))
                          (when (file-exists? generated-file)
                            (delete-file generated-file))))
                      (find-files "." "\\.pyx$"))
            (delete-file "MACS2/IO/CallPeakUnitPrecompiled.c")
            ;; Python 3.10 is in fact more recent than 3.6.
            (substitute* "setup.py"
              (("float\\(sys.version\\[:3\\]\\)<3.6") "False"))))))
    (build-system pyproject-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'set-HOME
           (lambda _ (setenv "HOME" "/tmp"))))))
    ;; Propagate these for use of macs as a library.
    (propagated-inputs
     (list python-cython python-numpy))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/macs3-project/MACS")
    (synopsis "Model based analysis for ChIP-Seq data")
    (description
     "MACS is an implementation of a ChIP-Seq analysis algorithm for
identifying transcript factor binding sites named Model-based Analysis of
ChIP-Seq (MACS).  MACS captures the influence of genome complexity to evaluate
the significance of enriched ChIP regions and it improves the spatial
resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
    (license license:bsd-3)))

(define-public maffilter
  (package
    (name "maffilter")
    (version "1.3.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/jydu/maffilter")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "196c16qw82niqqyzi7j1ga1n0zmir73bm26kg04m0i5aq2cpa0ml"))))
    (build-system cmake-build-system)
    (arguments (list #:tests? #false)) ;there are none
    (inputs
     (list boost
           bpp-core
           bpp-phyl
           bpp-phyl-omics
           bpp-seq
           bpp-seq-omics
           zlib))
    (home-page "https://jydu.github.io/maffilter/")
    (synopsis "Multiple alignment format file processor")
    (description
     "MafFilter is a program dedicated to the analysis of genome alignments.
It parses and manipulates @acronym{MAF, multiple alignment format} files as
well as more simple fasta files.  This package can be used to design a
pipeline as a series of consecutive filters, each performing a dedicated
analysis.  Many of the filters are available, from alignment cleaning to
phylogeny reconstruction and population genetics analysis.  Despite various
filtering options and format conversion tools, MafFilter can compute a wide
range of statistics (phylogenetic trees, nucleotide diversity, inferrence of
selection, etc.).")
    (license license:gpl3+)))

(define-public mafft
  (package
    (name "mafft")
    (version "7.475")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://mafft.cbrc.jp/alignment/software/mafft-" version
                    "-without-extensions-src.tgz"))
              (file-name (string-append name "-" version ".tgz"))
              (sha256
               (base32
                "0i2i2m3blh2xkbkdk48hxfssks30ny0v381gdl7zwhcvp0axs26r"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; no automated tests, though there are tests in the read me
       #:make-flags ,#~(list (string-append "PREFIX=" #$output)
                             (string-append "BINDIR="
                                            (string-append #$output "/bin")))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-dir
           (lambda _ (chdir "core") #t))
         (add-after 'enter-dir 'patch-makefile
           (lambda _
             ;; on advice from the MAFFT authors, there is no need to
             ;; distribute mafft-profile, mafft-distance, or
             ;; mafft-homologs.rb as they are too "specialised".
             (substitute* "Makefile"
               ;; remove mafft-homologs.rb from SCRIPTS
               (("^SCRIPTS = mafft mafft-homologs.rb")
                "SCRIPTS = mafft")
               ;; remove mafft-homologs from MANPAGES
               (("^MANPAGES = mafft.1 mafft-homologs.1")
                "MANPAGES = mafft.1")
               ;; remove mafft-distance from PROGS
               (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
                "PROGS = dvtditr dndfast7 dndblast sextet5")
               ;; remove mafft-profile from PROGS
               (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
                "splittbfast disttbfast tbfast f2cl mccaskillwrap")
               (("^rm -f mafft-profile mafft-profile.exe") "#")
               (("^rm -f mafft-distance mafft-distance.exe") ")#")
               ;; do not install MAN pages in libexec folder
               (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))))
         (add-after 'enter-dir 'patch-paths
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* '("pairash.c"
                            "mafft.tmpl")
               (("perl") (which "perl"))
               (("([\"`| ])awk" _ prefix)
                (string-append prefix (which "awk")))
               (("grep") (which "grep")))))
         (delete 'configure)
         (add-after 'install 'wrap-programs
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (path (string-append
                           (assoc-ref inputs "coreutils") "/bin:")))
               (for-each (lambda (file)
                           (wrap-program file
                             `("PATH" ":" prefix (,path))))
                         (find-files bin))))))))
    (inputs
     (list bash-minimal perl ruby gawk grep coreutils))
    (home-page "https://mafft.cbrc.jp/alignment/software/")
    (synopsis "Multiple sequence alignment program")
    (description
     "MAFFT offers a range of multiple alignment methods for nucleotide and
protein sequences.  For instance, it offers L-INS-i (accurate; for alignment
of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
sequences).")
    (license (license:non-copyleft
              "https://mafft.cbrc.jp/alignment/software/license.txt"
              "BSD-3 with different formatting"))))

(define-public mash
  (package
    (name "mash")
    (version "2.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/marbl/mash")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
              (modules '((guix build utils)))
              (snippet
               ;; Delete bundled kseq.
               ;; TODO: Also delete bundled murmurhash and open bloom filter.
               '(delete-file "src/mash/kseq.h"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; No tests.
       #:configure-flags
       ,#~(list
           (string-append "--with-capnp=" #$(this-package-input "capnproto"))
           (string-append "--with-gsl=" #$(this-package-input "gsl")))
       #:make-flags (list "CC=gcc")
       #:phases
       (modify-phases %standard-phases
         (replace 'bootstrap
           ;; The bootstrap script is missing a shebang.
           (lambda _
             (invoke "bash" "./bootstrap.sh")))
         (add-after 'unpack 'fix-includes
           (lambda _
             (substitute* '("src/mash/Sketch.cpp"
                            "src/mash/CommandFind.cpp"
                            "src/mash/CommandScreen.cpp")
               (("^#include \"kseq\\.h\"")
                "#include \"htslib/kseq.h\""))))
         (add-after 'fix-includes 'use-c++14
           (lambda _
             ;; capnproto 1.0 requires c++14 to build.
             (substitute* (list "configure.ac" "Makefile.in")
               (("c\\+\\+11") "c++14")))))))
    (native-inputs
     (list autoconf))
    (inputs
     (list ;; Capnproto and htslib are statically embedded in the final
           ;; application. Therefore we also list their licenses, below.
           capnproto
           htslib
           gsl
           zlib))
    (supported-systems '("x86_64-linux"))
    (home-page "https://mash.readthedocs.io")
    (synopsis "Fast genome and metagenome distance estimation using MinHash")
    (description "Mash is a fast sequence distance estimator that uses the
MinHash algorithm and is designed to work with genomes and metagenomes in the
form of assemblies or reads.")
    (license (list license:bsd-3          ; Mash
                   license:expat          ; HTSlib and capnproto
                   license:public-domain  ; MurmurHash 3
                   license:cpl1.0))))     ; Open Bloom Filter

(define-public metabat
  (package
    (name "metabat")
    (version "2.15")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://bitbucket.org/berkeleylab/metabat.git")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0v3gsps0ypani14102z2y1a2wignhpf7s1h45mxmj5f783rkhqd9"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       ,#~(list (string-append "-Dzlib_LIB=" #$(this-package-input "zlib")
                               "/lib/libz.so")
                (string-append "-Dhtslib_LIB=" #$(this-package-input "htslib")
                               "/lib/libhts.so")
                (string-append "-DBOOST_ROOT=" #$(this-package-input "boost")))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'configure-version-file
           (lambda _
             (copy-file "metabat_version.h.in" "metabat_version.h")
             (substitute* "metabat_version.h"
               (("@_time_stamp@") "19700101")
               (("@GIT_IS_DIRTY@") "0")
               (("@GIT_RETRIEVED_STATE@") "0")
               (("@GIT_HEAD_SHA1@") (string-append "v" ,version)))))
         (add-after 'unpack 'do-not-use-bundled-libraries
           (lambda _
             (substitute* "CMakeLists.txt"
               (("include\\(cmake.*") ""))
             (substitute* "src/CMakeLists.txt"
               (("set\\(Boost.*") "")
               (("add_dependencies.*") "")))))))
    (inputs
     (list zlib perl samtools htslib boost))
    (home-page "https://bitbucket.org/berkeleylab/metabat")
    (synopsis
     "Reconstruction of single genomes from complex microbial communities")
    (description
     "Grouping large genomic fragments assembled from shotgun metagenomic
sequences to deconvolute complex microbial communities, or metagenome binning,
enables the study of individual organisms and their interactions.  MetaBAT is
an automated metagenome binning software, which integrates empirical
probabilistic distances of genome abundance and tetranucleotide frequency.")
    ;; The source code contains inline assembly.
    (supported-systems '("x86_64-linux" "i686-linux"))
    (license (license:non-copyleft "file://license.txt"
                                   "See license.txt in the distribution."))))

(define-public metal
  (package
    (name "metal")
    (version "2011-03-25")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://csg.sph.umich.edu/abecasis/Metal/"
                           "download/generic-metal-" version ".tar.gz"))
       (sha256
        (base32
         "1bk00hc0xagmq0mabmbb8bykl75qd4kfyirba869h4x6hmn4a0f3"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f
      #:make-flags
      #~(list (string-append "INSTALLDIR=" #$output "/bin") "all")
      #:phases
      '(modify-phases %standard-phases
         (replace 'configure
           (lambda _
             (substitute* "Makefile"
               (("^CFLAGS=") "CFLAGS=-std=c++11 ")))))))
    (inputs (list zlib `(,zlib "static")))
    (home-page "http://csg.sph.umich.edu/abecasis/Metal/")
    (synopsis "Facilitate meta-analysis of large datasets")
    (description "METAL is a tool for meta-analysis genomewide association
scans.  METAL can combine either test statistics and standard errors or
p-values across studies (taking sample size and direction of effect into
account).  METAL analysis is a convenient alternative to a direct analysis of
merged data from multiple studies.  It is especially appropriate when data
from the individual studies cannot be analyzed together because of differences
in ethnicity, phenotype distribution, gender or constraints in sharing of
individual level data imposed.  Meta-analysis results in little or no loss of
efficiency compared to analysis of a combined dataset including data from all
individual studies.")
    (license license:bsd-3)))

(define-public minced
  (package
    (name "minced")
    (version "0.3.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/ctSkennerton/minced")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
    (build-system gnu-build-system)
    (arguments
     `(#:test-target "test"
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (add-before 'check 'fix-test
           (lambda _
             ;; Fix test for latest version.
             (substitute* "t/Aquifex_aeolicus_VF5.expected"
               (("minced:0.1.6") "minced:0.2.0"))
             #t))
         (replace 'install ; No install target.
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (wrapper (string-append bin "/minced")))
               ;; Minced comes with a wrapper script that tries to figure out where
               ;; it is located before running the JAR. Since these paths are known
               ;; to us, we build our own wrapper to avoid coreutils dependency.
               (install-file "minced.jar" bin)
               (with-output-to-file wrapper
                 (lambda _
                   (display
                    (string-append
                     "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
                     (assoc-ref inputs "jre") "/bin/java -jar "
                     bin "/minced.jar \"$@\"\n"))))
               (chmod wrapper #o555))
             #t)))))
    (native-inputs
     `(("jdk" ,icedtea "jdk")))
    (inputs
     `(("bash" ,bash)
       ("jre" ,icedtea "out")))
    (home-page "https://github.com/ctSkennerton/minced")
    (synopsis "Mining CRISPRs in Environmental Datasets")
    (description
     "MinCED is a program to find Clustered Regularly Interspaced Short
Palindromic Repeats (CRISPRs) in DNA sequences.  It can be used for
unassembled metagenomic reads, but is mainly designed for full genomes and
assembled metagenomic sequence.")
    (license license:gpl3+)))

(define-public muscle
  (package
    (name "muscle")
    (version "3.8.1551")
    (source (origin
              (method url-fetch/tarbomb)
              (uri (string-append
                    "http://www.drive5.com/muscle/muscle_src_"
                    version ".tar.gz"))
              (sha256
               (base32
                "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags (list "LDLIBS = -lm")
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'check
           ;; There are no tests, so just test if it runs.
           (lambda _ (invoke "./muscle" "-version") #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin")))
               (install-file "muscle" bin)
               #t))))))
    (home-page "http://www.drive5.com/muscle")
    (synopsis "Multiple sequence alignment program")
    (description
     "MUSCLE aims to be a fast and accurate multiple sequence alignment
program for nucleotide and protein sequences.")
    ;; License information found in 'muscle -h' and usage.cpp.
    (license license:public-domain)))

(define-public music
  (let ((commit "b1caecdb164b1ab80acccb9463abe2526a56f69f")
        (revision "1"))
    (package
      (name "music")
      (version (git-version "0.0.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/gersteinlab/MUSIC.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0arj300h8cpbya7y98g066xsxcg2a65h3y0qs250rlj072f1b4ia"))))
      (build-system gnu-build-system)
      (arguments
       (list
        #:tests? #f                     ; no "check" target
        #:phases
        #~(modify-phases %standard-phases
            (delete 'configure)
            ;; There is no "install" target.
            (replace 'install
              (lambda _
                (let ((bin (string-append #$output "/bin")))
                  (install-file "bin/MUSIC" bin)))))))
      (home-page "https://github.com/gersteinlab/MUSIC/")
      (synopsis "Multiscale enrichment calling for ChIP-Seq datasets")
      (description
       "MUSIC is an algorithm for identification of enriched regions at
multiple scales in the read depth signals from ChIP-Seq experiments.")
      ;; See https://github.com/gersteinlab/MUSIC/issues/6
      (license license:gpl2+))))

(define-public newick-utils
  ;; There are no recent releases so we package from git.
  (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
    (package
      (name "newick-utils")
      (version (string-append "1.6-1." (string-take commit 8)))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/tjunier/newick_utils")
                      (commit commit)))
                (file-name (string-append name "-" version "-checkout"))
                (sha256
                 (base32
                  "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? ,(not (or (target-riscv64?)   ;XXX: stuck on riscv64-linux
                            (%current-target-system)))
         #:make-flags (list "CFLAGS=-O2 -g -fcommon")))
      (inputs
       ;; XXX: TODO: Enable Lua and Guile bindings.
       ;; https://github.com/tjunier/newick_utils/issues/13
       (list libxml2 flex bison))
      (native-inputs
       (list autoconf automake libtool))
      (synopsis "Programs for working with newick format phylogenetic trees")
      (description
       "Newick-utils is a suite of utilities for processing phylogenetic trees
in Newick format.  Functions include re-rooting, extracting subtrees,
trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
      (home-page "https://github.com/tjunier/newick_utils")
      (license license:bsd-3))))

(define-public orfm
  (package
    (name "orfm")
    (version "0.7.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/wwood/OrfM/releases/download/v"
                    version "/orfm-" version ".tar.gz"))
              (sha256
               (base32
                "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
    (build-system gnu-build-system)
    (inputs (list zlib))
    (native-inputs
     (list ruby-bio-commandeer ruby-rspec ruby))
    (synopsis "Simple and not slow open reading frame (ORF) caller")
    (description
     "An ORF caller finds stretches of DNA that, when translated, are not
interrupted by stop codons.  OrfM finds and prints these ORFs.")
    (home-page "https://github.com/wwood/OrfM")
    (license license:lgpl3+)))

(define-public prank
  (package
    (name "prank")
    (version "170427")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://wasabiapp.org/download/prank/prank.source."
                    version ".tgz"))
              (sha256
               (base32
                "0nc8g9c5rkdxcir46s0in9ci1sxwzbjibxrvkksf22ybnplvagk2"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-src-dir
           (lambda _ (chdir "src")))
         (add-after 'unpack 'remove-m64-flag
           ;; Prank will build with the correct 'bit-ness' without this flag
           ;; and this allows building on 32-bit machines.
           (lambda _
             (substitute* "src/Makefile"
               (("-m64") ""))))
         (delete 'configure)
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (man (string-append out "/share/man/man1"))
                    (path (string-append
                           (assoc-ref inputs "mafft") "/bin:"
                           (assoc-ref inputs "exonerate") "/bin:"
                           (assoc-ref inputs "bppsuite") "/bin")))
               (install-file "prank" bin)
               (wrap-program (string-append bin "/prank")
                 `("PATH" ":" prefix (,path)))
               (install-file "prank.1" man)))))))
    (inputs
     (list mafft exonerate bppsuite))
    (home-page "http://wasabiapp.org/software/prank/")
    (synopsis "Probabilistic multiple sequence alignment program")
    (description
     "PRANK is a probabilistic multiple sequence alignment program for DNA,
codon and amino-acid sequences.  It is based on a novel algorithm that treats
insertions correctly and avoids over-estimation of the number of deletion
events.  In addition, PRANK borrows ideas from maximum likelihood methods used
in phylogenetics and correctly takes into account the evolutionary distances
between sequences.  Lastly, PRANK allows for defining a potential structure
for sequences to be aligned and then, simultaneously with the alignment,
predicts the locations of structural units in the sequences.")
    (license license:gpl2+)))

(define-public proteinortho
  (package
    (name "proteinortho")
    (version "6.3.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://gitlab.com/paulklemm_PHD/proteinortho.git")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0p8iaxq193fh67hw3cydvdah1vz1c3f18227gj1mhkww0ms7g6xa"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Remove pre-built scripts and source tarballs.
                  (delete-file-recursively "src/BUILD/")
                  (delete-file "src/lapack-3.8.0.tar.gz")))))
    (build-system gnu-build-system)
    (arguments
     (list
       #:test-target "test"
       #:parallel-tests? #f
       #:make-flags
       #~(list (string-append "CC=" #$(cc-for-target))
               (string-append "CXX=" #$(cxx-for-target))
               (string-append "PREFIX=" #$output)
               (string-append "INSTALLDIR=" #$output "/bin"))
       #:phases
       #~(modify-phases %standard-phases
           (delete 'configure)
           (add-before 'install 'make-install-directory
             ;; The install directory is not created during 'make install'.
             (lambda* (#:key outputs #:allow-other-keys)
               (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))
           (add-after 'install 'wrap-programs
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let ((path (getenv "PATH"))
                     (out (assoc-ref outputs "out"))
                     (guile (search-input-file inputs "bin/guile")))
                 (for-each (lambda (script)
                             (wrap-script script #:guile guile
                                          `("PATH" ":" prefix (,path))))
                           (cons (string-append out "/bin/proteinortho")
                                 (find-files out "\\.(pl|py)$")))))))))
    (inputs
     (list bash-minimal
           guile-3.0         ; for wrap-script
           diamond
           perl
           python-wrapper
           blast+
           openblas))
    (native-inputs
     (list which))
    (home-page "https://www.bioinf.uni-leipzig.de/Software/proteinortho")
    (synopsis "Detect orthologous genes across species")
    (description
     "Proteinortho is a tool to detect orthologous genes across different
species.  For doing so, it compares similarities of given gene sequences and
clusters them to find significant groups.  The algorithm was designed to handle
large-scale data and can be applied to hundreds of species at once.")
    (properties `((tunable? . #t)))
    (license license:gpl3+)))

(define-public prodigal
  (package
    (name "prodigal")
    ;; Check for a new home page when updating this package:
    ;; https://github.com/hyattpd/Prodigal/issues/36#issuecomment-536617588
    (version "2.6.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/hyattpd/Prodigal")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; no check target
       #:make-flags
       ,#~(list (string-append "INSTALLDIR=" #$output "/bin"))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (home-page "https://github.com/hyattpd/Prodigal")
    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
    (description
     "Prodigal runs smoothly on finished genomes, draft genomes, and
metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
partial genes, and identifies translation initiation sites.")
    (license license:gpl3+)))

(define-public roary
  (package
    (name "roary")
    (version "3.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
             version ".tar.gz"))
       (sha256
        (base32
         "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
    (build-system perl-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build)
         (replace 'check
           (lambda _
             ;; The tests are not run by default, so we run each test file
             ;; directly.
             (setenv "PATH" (string-append (getcwd) "/bin" ":"
                                           (getenv "PATH")))
             (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
                                               (getenv "PERL5LIB")))
             (for-each (lambda (file)
                         (display file)(display "\n")
                         (invoke "perl" file))
                       (find-files "t" ".*\\.t$"))))
         (replace 'install
           ;; There is no 'install' target in the Makefile.
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (perl (string-append out "/lib/perl5/site_perl"))
                    (roary-plots "contrib/roary_plots"))
               (mkdir-p bin)
               (mkdir-p perl)
               (copy-recursively "bin" bin)
               (copy-recursively "lib" perl))))
         (add-after 'install 'wrap-programs
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (perl5lib (getenv "PERL5LIB"))
                    (path (getenv "PATH")))
               (for-each (lambda (prog)
                           (let ((binary (string-append out "/" prog)))
                             (wrap-program binary
                               `("PERL5LIB" ":" prefix
                                 (,(string-append perl5lib ":" out
                                                  "/lib/perl5/site_perl"))))
                             (wrap-program binary
                               `("PATH" ":" prefix
                                 (,(string-append path ":" out "/bin"))))))
                         (find-files "bin" ".*[^R]$"))
               (let ((file
                      (string-append out "/bin/roary-create_pan_genome_plots.R"))
                     (r-site-lib (getenv "R_LIBS_SITE"))
                     (coreutils-path
                      (dirname (search-input-file inputs "bin/chmod"))))
                 (wrap-program file
                   `("R_LIBS_SITE" ":" prefix
                     (,(string-append r-site-lib ":" out "/site-library/"))))
                 (wrap-program file
                   `("PATH" ":" prefix
                     (,(string-append coreutils-path ":" out "/bin")))))))))))
    (native-inputs
     (list perl-env-path perl-test-files perl-test-most perl-test-output))
    (inputs
     (list bash-minimal
           perl-array-utils
           bioperl-minimal
           perl-digest-md5-file
           perl-exception-class
           perl-file-find-rule
           perl-file-grep
           perl-file-slurper
           perl-file-which
           perl-graph
           perl-graph-readwrite
           perl-log-log4perl
           perl-moose
           perl-perlio-utf8_strict
           perl-text-csv
           bedtools
           cd-hit
           blast+
           mcl
           parallel
           prank
           mafft
           fasttree
           grep
           sed
           gawk
           r-minimal
           r-ggplot2
           coreutils))
    (home-page "https://sanger-pathogens.github.io/Roary/")
    (synopsis "High speed stand-alone pan genome pipeline")
    (description
     "Roary is a high speed stand alone pan genome pipeline, which takes
annotated assemblies in GFF3 format (produced by the Prokka program) and
calculates the pan genome.  Using a standard desktop PC, it can analyse
datasets with thousands of samples, without compromising the quality of the
results.  128 samples can be analysed in under 1 hour using 1 GB of RAM and a
single processor.  Roary is not intended for metagenomics or for comparing
extremely diverse sets of genomes.")
    (license license:gpl3)))

(define-public raxml
  (package
    (name "raxml")
    (version "8.2.12")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/stamatak/standard-RAxML")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; There are no tests.
       ;; Use 'standard' Makefile rather than SSE or AVX ones.
       #:make-flags (list "-f" "Makefile.HYBRID.gcc")
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (executable "raxmlHPC-HYBRID"))
               (install-file executable bin)
               (symlink (string-append bin "/" executable) "raxml"))
             #t)))))
    (inputs
     (list openmpi))
    (home-page "https://cme.h-its.org/exelixis/web/software/raxml/index.html")
    (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
    (description
     "RAxML is a tool for phylogenetic analysis and post-analysis of large
phylogenies.")
    ;; The source includes x86 specific code
    (supported-systems '("x86_64-linux" "i686-linux"))
    (license license:gpl2+)))

(define-public rsem
  (package
    (name "rsem")
    (version "1.3.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/deweylab/RSEM")
             (commit (string-append "v" version))))
       (sha256
        (base32 "1yl4i7z20n2p84j1lmk15aiak3yqc6fiw0q5a4pndw7pxfiq3rzp"))
       (file-name (git-file-name name version))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; remove bundled copy of boost and samtools
           (delete-file-recursively "boost")
           (delete-file-recursively "samtools-1.3")))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:make-flags
       ,#~(list (string-append "BOOST="
                               #$(this-package-input "boost")
                               "/include/")
                (string-append "SAMHEADERS="
                               #$(this-package-input "htslib")
                               "/include/htslib/sam.h")
                (string-append "SAMLIBS="
                               #$(this-package-input "htslib")
                               "/lib/libhts.so"))
       #:phases
       (modify-phases %standard-phases
         ;; No "configure" script.
         (replace 'configure
           (lambda _
             (substitute* "Makefile"
               (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
               ;; Do not build bundled samtools library.
               (("^\\$\\(SAMLIBS\\).*") "")
               ;; Needed for Boost
               (("gnu\\+\\+98") "gnu++11"))
             ;; C++11 compatibility
             (substitute* "buildReadIndex.cpp"
               (("success = \\(getline")
                "success = (bool)(getline"))
             (substitute* '("PairedEndHit.h"
                            "SingleHit.h")
               (("return \\(in>>sid>>pos")
                "return (bool)(in>>sid>>pos"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (string-append (assoc-ref outputs "out")))
                    (bin (string-append out "/bin/"))
                    (perl (string-append out "/lib/perl5/site_perl")))
               (mkdir-p bin)
               (mkdir-p perl)
               (for-each (lambda (file)
                           (install-file file bin))
                         (find-files "." "rsem-.*"))
               (install-file "rsem_perl_utils.pm" perl))))
         (add-after 'install 'wrap-program
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (for-each (lambda (prog)
                           (wrap-program (string-append out "/bin/" prog)
                             `("PERL5LIB" ":" prefix
                               (,(string-append out "/lib/perl5/site_perl")))))
                         '("rsem-calculate-expression"
                           "rsem-control-fdr"
                           "rsem-generate-data-matrix"
                           "rsem-generate-ngvector"
                           "rsem-plot-transcript-wiggles"
                           "rsem-prepare-reference"
                           "rsem-run-ebseq"
                           "rsem-run-prsem-testing-procedure"))))))))
    (inputs
     (list bash-minimal boost r-minimal perl htslib-1.3 zlib))
    (home-page "https://deweylab.biostat.wisc.edu/rsem/")
    (synopsis "Estimate gene expression levels from RNA-Seq data")
    (description
     "RSEM is a software package for estimating gene and isoform expression
levels from RNA-Seq data.  The RSEM package provides a user-friendly
interface, supports threads for parallel computation of the EM algorithm,
single-end and paired-end read data, quality scores, variable-length reads and
RSPD estimation.  In addition, it provides posterior mean and 95% credibility
interval estimates for expression levels.  For visualization, it can generate
BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
    (license license:gpl3+)))

(define-public rseqc
  (package
    (name "rseqc")
    (version "3.0.1")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/rseqc/"
                       "RSeQC-" version ".tar.gz"))
       (sha256
        (base32
         "0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
    (build-system python-build-system)
    (inputs
     (list python-cython
           python-bx-python
           python-pybigwig
           python-pysam
           python-numpy
           zlib))
    (native-inputs
     (list python-nose))
    (home-page "https://rseqc.sourceforge.net/")
    (synopsis "RNA-seq quality control package")
    (description
     "RSeQC provides a number of modules that can comprehensively evaluate
high throughput sequence data, especially RNA-seq data.  Some basic modules
inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
while RNA-seq specific modules evaluate sequencing saturation, mapped reads
distribution, coverage uniformity, strand specificity, etc.")
    (license license:gpl3+)))

(define-public seek
  ;; There are no release tarballs.  And the installation instructions at
  ;; http://seek.princeton.edu/installation.jsp only mention a mercurial
  ;; changeset ID.  This is a git repository, though.  So we just take the
  ;; most recent commit.
  (let ((commit "196ed4c7633246e9c628e4330d77577ccfd7f1e5")
        (revision "1"))
    (package
      (name "seek")
      (version (git-version "1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/FunctionLab/sleipnir.git")
                      (commit commit)
                      (recursive? #true)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0c658n8nz563a96dsi4gl2685vxph0yfmmqq5yjc6i4xin1jy1ab"))))
      (build-system cmake-build-system)
      (arguments
       `(#:configure-flags
         ,#~(list (string-append "-DSVM_LIBRARY="
                                 #$(this-package-input "libsvm")
                                 "/lib/libsvm.so.2")
                  (string-append "-DSVM_INCLUDE="
                                 #$(this-package-input "libsvm")
                                 "/include"))
         #:tests? #false ; tests only fail in the build container
         #:phases
         (modify-phases %standard-phases
           ;; The check phase expects to find the unit_tests executable in the
           ;; "build/bin" directory, but it is actually in "build/tests".
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
                 (invoke "tests/unit_tests")))))))
      (inputs
       `(("apache-thrift:include" ,apache-thrift "include")
         ("apache-thrift:lib" ,apache-thrift "lib")
         ("gsl" ,gsl)
         ("boost" ,boost)
         ("gengetopt" ,gengetopt)
         ("libsvm" ,libsvm)
         ("log4cpp" ,log4cpp)
         ("python" ,python)
         ("readline" ,readline)))
      (native-inputs
       (list pkg-config))
      (home-page "https://seek.princeton.edu")
      (synopsis "Gene co-expression search engine")
      (description
       "SEEK is a computational gene co-expression search engine.  SEEK provides
biologists with a way to navigate the massive human expression compendium that
now contains thousands of expression datasets.  SEEK returns a robust ranking
of co-expressed genes in the biological area of interest defined by the user's
query genes.  It also prioritizes thousands of expression datasets according
to the user's query of interest.")
      (license license:cc-by3.0))))

(define-public samtools
  (package
    (name "samtools")
    (version "1.19")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "https://github.com/samtools/samtools"
                       "/releases/download/" version
                       "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "10wby07w33rfypy4kf73v9wwnbyh0lrazbsmrgrvcl88w8c3nszs"))
       (modules '((guix build utils)))
       ;; Delete bundled htslib.
       (snippet '(delete-file-recursively "htslib-1.19"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags (list "--with-ncurses")
       ;; The samtools test suite (and software) expects SSE-based math, even on
       ;; i686-linux, and not 387-based math.  Adjust the CPPFLAGS accordingly.
       ,@(if (target-x86-32?)
             `(#:make-flags (list "CPPFLAGS = -msse -mfpmath=sse"))
             '())
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-tests
           (lambda _
             (substitute* "test/test.pl"
               ;; The test script calls out to /bin/bash
               (("/bin/bash") (which "bash"))))))))
    (native-inputs (list pkg-config))
    (inputs
     (list htslib ncurses perl python zlib))
    (home-page "https://samtools.sourceforge.net")
    (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
    (description
     "Samtools implements various utilities for post-processing nucleotide
sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
    (license license:expat)))

(define-public samtools-1.14
  (package/inherit samtools
    (version "1.14")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "0x3xdda78ac5vx66b3jdsv9sfhyz4npl4znl1zbaf3lbm6xdlhck"))
       (modules '((guix build utils)))
       (snippet '(begin
                   ;; Delete bundled htslib.
                   (delete-file-recursively "htslib-1.14")))))
    (native-inputs (list pkg-config))
    (inputs
     (list htslib-1.14 ncurses perl python zlib))))

(define-public samtools-1.12
  (package/inherit samtools
    (version "1.12")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
       (modules '((guix build utils)))
       (snippet '(begin
                   ;; Delete bundled htslib.
                   (delete-file-recursively "htslib-1.12")))))
    (arguments
     (substitute-keyword-arguments (package-arguments samtools)
       ((#:modules _ #f)
        '((ice-9 ftw)
          (ice-9 regex)
          (guix build gnu-build-system)
          (guix build utils)))
       ((#:phases phases)
        `(modify-phases ,phases
           (add-after 'install 'install-library
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
                 (install-file "libbam.a" lib))))
           (add-after 'install 'install-headers
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((include (string-append (assoc-ref outputs "out")
                                             "/include/samtools/")))
                 (for-each (lambda (file)
                             (install-file file include))
                           (scandir "." (lambda (name)
                                          (string-match "\\.h$" name)))))))))))
    (native-inputs (list pkg-config))
    (inputs
     (list htslib-1.12 ncurses perl python zlib))))

(define-public samtools-1.10
  (package (inherit samtools)
    (name "samtools")
    (version "1.10")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv"))
       (modules '((guix build utils)))
       (snippet '(begin
                   ;; Delete bundled htslib.
                   (delete-file-recursively "htslib-1.10")
                   #t))))
    (inputs
     (list htslib-1.10 ncurses perl python zlib))))

(define-public samtools-1.2
  (package (inherit samtools)
    (name "samtools")
    (version "1.2")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))
       (modules '((guix build utils)))
       (snippet
        ;; Delete bundled htslib and Windows binaries
        '(for-each delete-file-recursively (list "win32" "htslib-1.2.1")))))
    (arguments
     `(#:make-flags
       ,#~(list (string-append "prefix=" #$output)
                (string-append "BGZIP="
                               #$(this-package-input "htslib")
                               "/bin/bgzip")
                (string-append "HTSLIB="
                               #$(this-package-input "htslib")
                               "/lib/libhts.so")
                (string-append "HTSDIR="
                               #$(this-package-input "htslib")
                               "/include"))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-makefile-curses
           (lambda _
             (substitute* "Makefile"
               (("-lcurses") "-lncurses")
               (("include \\$\\(HTSDIR.*") ""))))
         (add-after 'unpack 'patch-tests
           (lambda _
             (substitute* "test/test.pl"
               ;; The test script calls out to /bin/bash
               (("/bin/bash") (which "bash"))
               ;; There are two failing tests upstream relating to the "stats"
               ;; subcommand in test_usage_subcommand ("did not have Usage"
               ;; and "usage did not mention samtools stats"), so we disable
               ;; them.
               (("(test_usage_subcommand\\(.*\\);)" cmd)
                (string-append "unless ($subcommand eq 'stats') {" cmd "};")))
             ;; This test fails because the grep output doesn't look as
             ;; expected; it is correct, though.
             (substitute* "test/mpileup/mpileup.reg"
               (("P 52.out.*") ""))))
         (delete 'configure))))
    (native-inputs
     (list grep gawk pkg-config))
    (inputs
     (list htslib-for-samtools-1.2 ncurses perl python zlib))))

(define-public samtools-0.1
  ;; This is the most recent version of the 0.1 line of samtools.  The input
  ;; and output formats differ greatly from that used and produced by samtools
  ;; 1.x and is still used in many bioinformatics pipelines.
  (package (inherit samtools)
    (version "0.1.19")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
    (arguments
     `(#:tests? #f ;no "check" target
       #:make-flags
       (list "LIBCURSES=-lncurses")
       ,@(substitute-keyword-arguments (package-arguments samtools)
           ((#:modules _ #f)
            '((ice-9 ftw)
              (ice-9 regex)
              (guix build gnu-build-system)
              (guix build utils)))
           ((#:phases phases)
            `(modify-phases ,phases
               (replace 'install
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let ((bin (string-append
                               (assoc-ref outputs "out") "/bin")))
                     (mkdir-p bin)
                     (install-file "samtools" bin)
                     #t)))
               (add-after 'install 'install-library
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
                     (install-file "libbam.a" lib))))
               (add-after 'install 'install-headers
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let ((include (string-append (assoc-ref outputs "out")
                                                 "/include/samtools/")))
                     (for-each (lambda (file)
                                 (install-file file include))
                               (scandir "." (lambda (name)
                                              (string-match "\\.h$" name)))))))
               (delete 'patch-tests)
               (delete 'configure))))))))

(define-public savvy
  (package
    (name "savvy")
    (version "2.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/statgen/savvy")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "03jh89gl67adnpkwx8yrdn62pd9sg69k21gxh15my2vvpfl1pxlx"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      '(list "-DBUILD_TESTS=ON"
             "-DBUILD_EVAL=ON")
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'use-shared-libraries
           (lambda _
             ;; Do not prefer static libraries.
             (substitute* "CMakeLists.txt"
               (("set\\(CMAKE_FIND_LIBRARY_SUFFIXES \".a;.*") "")))))))
    (native-inputs (list pkg-config))
    (inputs (list htslib))
    (propagated-inputs (list streambuf-shrinkwrap))
    (home-page "https://github.com/statgen/savvy/")
    (synopsis "Interface to various variant calling formats")
    (description
     "Savvy is the official C++ interface for the SAV file format and offers
seamless support for BCF and VCF files.")
    (license license:mpl2.0)))

(define-public morpheus
  (package
    (name "morpheus")
    (version "2.3.6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://gitlab.com/morpheus.lab/morpheus")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1jyzbkz8d39kjicrk3ihcx7yvq5wsynvnlcw922bqqsw8nwnn12c"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           (delete-file-recursively "3rdparty/eigen")
           (substitute* '("morpheus/core/cpm_shape_tracker.cpp"
                          "morpheus/core/membranemapper.h"
                          "morpheus/testing/components/motility/directed_motion_test.cpp"
                          "morpheus/testing/components/interaction/generator_cell_sorting.cpp"
                          "morpheus/testing/components/interaction/test_cell_sorting.cpp"
                          "morpheus/testing/core/cpm/generator_csm_plane.cpp"
                          "morpheus/testing/test_operators.h")
             (("#include \"eigen/") "#include \"eigen3/"))))))
    ;; This is for a different Morpheus.
    (properties '((lint-hidden-cve "CVE-2022-31261")))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      '(list "-DMORPHEUS_GUI=OFF"
             "-DBUILD_TESTING=ON"
             "-DDOWNLOAD_XTENSOR=OFF")
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'disable-gtest-download
           (lambda _
             (substitute* "3rdparty/CMakeLists.txt"
               (("add_subdirectory\\(GTest\\)") ""))))
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "ctest" "--output-junit" "test_results.xml")))))))
    (inputs (list boost
                  eigen
                  file
                  gnuplot
                  libtiff
                  libxslt
                  xsimd
                  xtensor
                  xtl
                  zlib))
    (native-inputs
     (list doxygen googletest xxd))
    (home-page "https://gitlab.com/morpheus.lab/morpheus")
    (synopsis "Multicellular simulation")
    (description
     "Morpheus is a modeling and simulation environment for the study of
multi-scale and multicellular systems.")
    (license license:bsd-3)))

(define-public mosaik
  (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
    (package
      (name "mosaik")
      (version "2.2.30")
      (source (origin
                ;; There are no release tarballs nor tags.
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/wanpinglee/MOSAIK")
                      (commit commit)))
                (file-name (string-append name "-" version))
                (sha256
                 (base32
                  "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; no tests
         #:make-flags (list "CC=gcc")
         #:phases
         (modify-phases %standard-phases
           (replace 'configure
                    (lambda _ (chdir "src") #t))
           (replace 'install
                    (lambda* (#:key outputs #:allow-other-keys)
                      (let ((bin (string-append (assoc-ref outputs "out")
                                                "/bin")))
                        (mkdir-p bin)
                        (copy-recursively "../bin" bin)
                        #t))))))
      (inputs
       `(("perl" ,perl)
         ("zlib:static" ,zlib "static")
         ("zlib" ,zlib)))
      (supported-systems '("x86_64-linux"))
      (home-page "https://github.com/wanpinglee/MOSAIK")
      (synopsis "Map nucleotide sequence reads to reference genomes")
      (description
       "MOSAIK is a program for mapping second and third-generation sequencing
reads to a reference genome.  MOSAIK can align reads generated by all the
major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
      ;; MOSAIK is released under the GPLv2+ with the exception of third-party
      ;; code released into the public domain:
      ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
      ;; 2. MD5 implementation - RSA Data Security, RFC 1321
      (license (list license:gpl2+ license:public-domain)))))

(define-public mosaicatcher
  (package
    (name "mosaicatcher")
    (version "0.3.1")
    (source (origin
              ;; There are no release tarballs nor tags.
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/friendsofstrandseq/mosaicatcher")
                    (commit (string-append version "-dev"))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd"))
              (patches (search-patches "mosaicatcher-unbundle-htslib.patch"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #false ; there are no tests
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _ (chdir "src")))
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((target (assoc-ref outputs "out"))
                    (bin (string-append target "/bin"))
                    (share (string-append target "/share/mosaicatcher")))
               (install-file "mosaic" bin)
               (mkdir-p share)
               (copy-recursively "../R" share)))))))
    (inputs
     (list boost htslib))
    (home-page "https://github.com/friendsofstrandseq/mosaicatcher")
    (synopsis "Count and classify Strand-seq reads")
    (description
     "Mosaicatcher counts Strand-seq reads and classifies strand states of
each chromosome in each cell using a Hidden Markov Model.")
    (license license:expat)))

(define-public ngs-sdk
  (package
    (name "ngs-sdk")
    (version "2.10.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/ncbi/ngs")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1ix51c25hjn57w93qmwzw80xh2i34wx8j2hn7szh8p6w8i3az5qa"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-build? #f ; not supported
       #:tests? #f ; no "check" target
       #:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               ;; Allow 'konfigure.perl' to find 'package.prl'.
               (setenv "PERL5LIB"
                       (string-append ".:" (getenv "PERL5LIB")))

               ;; The 'configure' script doesn't recognize things like
               ;; '--enable-fast-install'.
               (invoke "./configure"
                       (string-append "--build-prefix=" (getcwd) "/build")
                       (string-append "--prefix=" out))
               #t)))
         (add-after 'unpack 'enter-dir
           (lambda _ (chdir "ngs-sdk") #t)))))
    (native-inputs (list perl))
    ;; According to the test
    ;;   unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
    ;; in ngs-sdk/setup/konfigure.perl
    (supported-systems '("i686-linux" "x86_64-linux"))
    (home-page "https://github.com/ncbi/ngs")
    (synopsis "API for accessing Next Generation Sequencing data")
    (description
     "NGS is a domain-specific API for accessing reads, alignments and pileups
produced from Next Generation Sequencing.  The API itself is independent from
any particular back-end implementation, and supports use of multiple back-ends
simultaneously.")
    (license license:public-domain)))

(define-public java-ngs
  (package (inherit ngs-sdk)
    (name "java-ngs")
    (arguments
     `(,@(substitute-keyword-arguments
             `(#:modules ((guix build gnu-build-system)
                          (guix build utils)
                          (srfi srfi-1)
                          (srfi srfi-26))
                         ,@(package-arguments ngs-sdk))
           ((#:phases phases)
            `(modify-phases ,phases
               (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
    (inputs
     `(("jdk" ,icedtea "jdk")
       ("ngs-sdk" ,ngs-sdk)))
    (synopsis "Java bindings for NGS SDK")))

(define-public ncbi-vdb
  (package
    (name "ncbi-vdb")
    (version "2.10.6")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/ncbi/ncbi-vdb")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:parallel-build? #f              ; not supported
      #:tests? #f                       ; no "check" target
      #:make-flags '(list "HAVE_HDF5=1")
      #:phases
      #~(modify-phases %standard-phases
          #;
          (add-after 'unpack 'make-files-writable
            (lambda _ (for-each make-file-writable (find-files "." ".*"))))
          (add-before 'configure 'set-perl-search-path
            (lambda _
              ;; Work around "dotless @INC" build failure.
              (setenv "PERL5LIB"
                      (string-append (getcwd) "/setup:"
                                     (getenv "PERL5LIB")))))
          ;; See https://github.com/ncbi/ncbi-vdb/issues/14
          (add-after 'unpack 'patch-krypto-flags
            (lambda _
              (substitute* "libs/krypto/Makefile"
                (("-Wa,-march=generic64\\+aes") "")
                (("-Wa,-march=generic64\\+sse4") ""))))
          (replace 'configure
            (lambda _
              ;; Override include path for libmagic
              (substitute* "setup/package.prl"
                (("name => 'magic', Include => '/usr/include'")
                 (string-append "name=> 'magic', Include => '"
                                #$(this-package-input "file")
                                "/include" "'")))

              ;; Install kdf5 library (needed by sra-tools)
              (substitute* "build/Makefile.install"
                (("LIBRARIES_TO_INSTALL =")
                 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))

              (substitute* "build/Makefile.env"
                (("CFLAGS	=" prefix)
                 (string-append prefix "-msse2 ")))

              ;; Override search path for ngs-java
              (substitute* "setup/package.prl"
                (("/usr/local/ngs/ngs-java")
                 #$(this-package-input "java-ngs")))

              ;; The 'configure' script doesn't recognize things like
              ;; '--enable-fast-install'.
              (invoke "./configure"
                      (string-append "--build-prefix=" (getcwd) "/build")
                      (string-append "--prefix=" #$output)
                      (string-append "--debug")
                      (string-append "--with-xml2-prefix="
                                     #$(this-package-input "libxml2"))
                      (string-append "--with-ngs-sdk-prefix="
                                     #$(this-package-input "ngs-sdk"))
                      (string-append "--with-hdf5-prefix="
                                     #$(this-package-input "hdf5")))))
          (add-after 'install 'install-interfaces
            (lambda _
              ;; Install interface libraries.  On i686 the interface libraries
              ;; are installed to "linux/gcc/i386", so we need to use the Linux
              ;; architecture name ("i386") instead of the target system prefix
              ;; ("i686").
              (mkdir (string-append #$output "/ilib"))
              (copy-recursively (string-append
                                 "build/ncbi-vdb/linux/gcc/"
                                 #$(platform-linux-architecture
                                    (lookup-platform-by-target-or-system
                                     (or (%current-target-system)
                                         (%current-system))))
                                 "/rel/ilib")
                                (string-append #$output "/ilib"))
              ;; Install interface headers
              (copy-recursively "interfaces"
                                (string-append #$output "/include"))))
          (add-after 'install-interfaces 'install-libs
            (lambda _
              (copy-recursively (string-append
                                 "build/ncbi-vdb/linux/gcc/"
                                 #$(platform-linux-architecture
                                    (lookup-platform-by-target-or-system
                                     (or (%current-target-system)
                                         (%current-system))))
                                 "/rel/lib")
                                (string-append #$output "/lib"))))
          ;; These files are needed by sra-tools.
          (add-after 'install 'install-configuration-files
            (lambda _
              (let ((target (string-append #$output "/kfg")))
                (mkdir target)
                (install-file "libs/kfg/default.kfg" target)
                (install-file "libs/kfg/certs.kfg" target)))))))
    (inputs
     (list file hdf5 java-ngs libxml2 ngs-sdk ))
    (native-inputs (list perl))
    ;; NCBI-VDB requires SSE capability.
    (supported-systems '("i686-linux" "x86_64-linux"))
    (home-page "https://github.com/ncbi/ncbi-vdb")
    (synopsis "Database engine for genetic information")
    (description
     "The NCBI-VDB library implements a highly compressed columnar data
warehousing engine that is most often used to store genetic information.
Databases are stored in a portable image within the file system, and can be
accessed/downloaded on demand across HTTP.")
    (license license:public-domain)))

(define-public plink
  (package
    (name "plink")
    (version "1.07")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://zzz.bwh.harvard.edu/plink/dist/plink-"
             version "-src.zip"))
       (sha256
        (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
       (patches (search-patches "plink-1.07-unclobber-i.patch"
                                "plink-endian-detection.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:make-flags ,#~(list (string-append "LIB_LAPACK="
                                            #$(this-package-input "openblas")
                                            "/lib/libopenblas.so")
                             "WITH_LAPACK=1"
                             "FORCE_DYNAMIC=1"
                             ;; disable phoning home
                             "WITH_WEBCHECK=")
       #:phases
       (modify-phases %standard-phases
         ;; no "configure" script
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out")
                                       "/bin/")))
               (install-file "plink" bin)))))))
    (inputs
     (list zlib openblas))
    (native-inputs
     (list unzip gcc-8))
    (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
    (synopsis "Whole genome association analysis toolset")
    (description
     "PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data).  Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
    ;; Code is released under GPLv2, except for fisher.h, which is under
    ;; LGPLv2.1+
    (license (list license:gpl2 license:lgpl2.1+))))

(define-public plink-ng
  (package (inherit plink)
    (name "plink-ng")
    (version "2.00a3.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/chrchang/plink-ng")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0m8wkyvbgvcr5kzc284w8fbhpxwglh2c1xq0yc3yv00a53gs7rv0"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files
      #:make-flags
      #~(list "BLASFLAGS=-lopenblas"
              "NO_SSE42=1"
              "NO_AVX2=1"
              "STATIC_ZSTD="
              (string-append "CC=" #$(cc-for-target))
              (string-append "PREFIX=" #$output)
              "DESTDIR=")
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _ (chdir "2.0/build_dynamic")))
         (delete 'configure)            ; no "configure" script
         (replace 'check
           (lambda* (#:key tests? inputs #:allow-other-keys)
             (when tests?
               (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
               (with-directory-excursion "../Tests"
                 (substitute* "run_tests.sh"
                   (("^./run_tests" m)
                    (string-append (which "bash") " " m)))
                 (invoke "bash" "run_tests.sh")))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (install-file "plink2"
                           (string-append
                            (assoc-ref outputs "out") "/bin")))))))
    (inputs
     (list openblas zlib `(,zstd "lib")))
    (native-inputs
     (list diffutils plink python simde)) ; for tests
    (home-page "https://www.cog-genomics.org/plink/")
    (license license:gpl3+)))

(define-public smithlab-cpp
  (let ((revision "1")
        (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
    (package
      (name "smithlab-cpp")
      (version (string-append "0." revision "." (string-take commit 7)))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/smithlabcode/smithlab_cpp")
                      (commit commit)))
                (file-name (string-append name "-" version "-checkout"))
                (sha256
                 (base32
                  "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
      (build-system gnu-build-system)
      (arguments
       `(#:modules ((guix build gnu-build-system)
                    (guix build utils)
                    (srfi srfi-26))
         #:tests? #f ;no "check" target
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'use-samtools-headers
            (lambda _
              (substitute* '("SAM.cpp"
                             "SAM.hpp")
                (("sam.h") "samtools/sam.h"))
              #t))
           (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out     (assoc-ref outputs "out"))
                     (lib     (string-append out "/lib"))
                     (include (string-append out "/include/smithlab-cpp")))
                (mkdir-p lib)
                (mkdir-p include)
                (for-each (cut install-file <> lib)
                          (find-files "." "\\.o$"))
                (for-each (cut install-file <> include)
                          (find-files "." "\\.hpp$")))
              #t))
           (delete 'configure))))
      (inputs
       (list samtools-0.1 zlib))
      (home-page "https://github.com/smithlabcode/smithlab_cpp")
      (synopsis "C++ helper library for functions used in Smith lab projects")
      (description
       "Smithlab CPP is a C++ library that includes functions used in many of
the Smith lab bioinformatics projects, such as a wrapper around Samtools data
structures, classes for genomic regions, mapped sequencing reads, etc.")
      (license license:gpl3+))))

(define-public preseq
  (package
    (name "preseq")
    (version "2.0.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/smithlabcode/preseq/"
                                  "releases/download/v" version
                                  "/preseq_v" version ".tar.bz2"))
              (sha256
               (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
              (modules '((guix build utils)))
              ;; Remove bundled samtools.
              (snippet '(delete-file-recursively "samtools"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))
       #:make-flags
       ,#~(list (string-append "PREFIX=" #$output)
                (string-append "LIBBAM="
                               #$(this-package-input "samtools")
                               "/lib/libbam.a")
                (string-append "SMITHLAB_CPP="
                               #$(this-package-input "smithlab-cpp")
                               "/lib")
                "PROGS=preseq"
                "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
    (inputs
     (list gsl samtools-0.1 smithlab-cpp zlib))
    (home-page "http://smithlabresearch.org/software/preseq/")
    (synopsis "Program for analyzing library complexity")
    (description
     "The preseq package is aimed at predicting and estimating the complexity
of a genomic sequencing library, equivalent to predicting and estimating the
number of redundant reads from a given sequencing depth and how many will be
expected from additional sequencing using an initial sequencing experiment.
The estimates can then be used to examine the utility of further sequencing,
optimize the sequencing depth, or to screen multiple libraries to avoid low
complexity samples.")
    (license license:gpl3+)))

(define-public python-screed
  (package
    (name "python-screed")
    (version "1.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "screed" version))
       (sha256
        (base32 "0slva743xn93h4sl5zg2as4ricnnj5pp6nw9dm4qclk4i9xglkvk"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-pytest-cov
           python-pytest-runner))
    (home-page "https://github.com/dib-lab/screed/")
    (synopsis "Short read sequence database utilities")
    (description "Screed parses FASTA and FASTQ files and generates databases.
Values such as sequence name, sequence description, sequence quality and the
sequence itself can be retrieved from these databases.")
    (license license:bsd-3)))

(define-public python-slamdunk
  (package
    (name "python-slamdunk")
    (version "0.4.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/t-neumann/slamdunk")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0lv3h5k2pn1pz35kz0wk5xmricxzy8qscs2y7nwh0k6x4pn0m0s5"))))
    (build-system python-build-system)
    (propagated-inputs
     (list python-biopython
           python-intervaltree
           python-joblib
           python-pandas
           python-pybedtools
           python-pysam))
    (native-inputs
     (list python-cython python-pytest))
    (home-page "https://t-neumann.github.io/slamdunk/")
    (synopsis "Streamline SLAM-seq analysis with high sensitivity")
    (description "SlamDunk is a fully automated tool for automated, robust,
scalable and reproducible SLAMseq data analysis.  Diagnostic plotting features
and a MultiQC plugin will make your SLAMseq data ready for immediate QA and
interpretation.")
    (license license:agpl3+)))

(define-public python-taggd
  (package
    (name "python-taggd")
    (version "0.3.6")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/SpatialTranscriptomicsResearch/taggd")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0j19ah81z7aqrdljah9hyarp91gvgbk63pz6fz3pdpksy1yqyi6k"))
              (modules '((guix build utils)))
              (snippet
               '(for-each delete-file
                          (find-files "taggd" "\\.c$")))))
    (build-system python-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'disable-broken-tests
           (lambda _
             (substitute* "tests/taggd_demultiplex_test.py"
               (("def test_normal_bam_run")
                "def _disabled_test_normal_bam_run")))))))
    (propagated-inputs
     (list python-numpy python-pysam python-setuptools))
    (native-inputs
     (list python-cython))
    (home-page "https://github.com/SpatialTranscriptomicsResearch/taggd")
    (synopsis "Genetic barcode demultiplexing")
    (description "This package provides TagGD barcode demultiplexing utilities
for Spatial Transcriptomics data.")
    (license license:bsd-3)))

(define-public stpipeline
  (package
    (name "stpipeline")
    (version "1.8.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "stpipeline" version))
              (sha256
               (base32
                "0har2g42fvaqpiz66lincy86aj1hvwzds26kxhxfamvyvv4721wk"))))
    (build-system python-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "requirements.txt"
               (("argparse.*") "")))))))
    (propagated-inputs
     (list htseq
           python-cython
           python-invoke
           python-numpy
           python-pandas
           python-pympler
           python-pysam
           python-regex
           python-scikit-learn
           python-scipy
           python-seaborn
           python-setuptools
           python-sqlitedict
           python-taggd
           samtools
           star))
    (home-page "https://github.com/SpatialTranscriptomicsResearch/st_pipeline")
    (synopsis "Pipeline for spatial mapping of unique transcripts")
    (description
     "This package provides an automated pipeline for spatial mapping of
unique transcripts.")
    (license license:expat)))

(define-public sra-tools
  (package
    (name "sra-tools")
    (version "2.10.6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/ncbi/sra-tools")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:parallel-build? #f             ; not supported
      #:tests? #f                      ; no "check" target
      #:make-flags
      #~(list (string-append "DEFAULT_CRT="
                             #$(this-package-input "ncbi-vdb")
                             "/kfg/certs.kfg")
              (string-append "DEFAULT_KFG="
                             #$(this-package-input "ncbi-vdb")
                             "/kfg/default.kfg")
              (string-append "VDB_LIBDIR="
                             #$(this-package-input "ncbi-vdb")
                             #$(if (string-prefix? "x86_64"
                                                   (or (%current-target-system)
                                                       (%current-system)))
                                   "/lib64"
                                   "/lib32")))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'configure 'set-perl-search-path
             (lambda _
               ;; Work around "dotless @INC" build failure.
               (setenv "PERL5LIB"
                       (string-append (getcwd) "/setup:"
                                      (getenv "PERL5LIB")))))
           (replace 'configure
             (lambda* (#:key inputs outputs #:allow-other-keys)
               ;; The build system expects a directory containing the sources and
               ;; raw build output of ncbi-vdb, including files that are not
               ;; installed.  Since we are building against an installed version of
               ;; ncbi-vdb, the following modifications are needed.
               (substitute* "setup/konfigure.perl"
                 ;; Make the configure script look for the "ilib" directory of
                 ;; "ncbi-vdb" without first checking for the existence of a
                 ;; matching library in its "lib" directory.
                 (("^            my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
                  "my $f = File::Spec->catdir($ilibdir, $ilib);")
                 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
                 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
                  "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))

               ;; Dynamic linking
               (substitute* "tools/copycat/Makefile"
                 (("smagic-static") "lmagic"))
               (substitute* "tools/driver-tool/utf8proc/Makefile"
                 (("CC\\?=gcc") "myCC=gcc")
                 (("\\(CC\\)") "(myCC)"))

               ;; Don't link libxml2 statically
               (substitute* "build/ld.linux.exe.sh"
                 (("grep -q 'OS_DISTRIBUTOR = Ubuntu.*") "true\n"))

               ;; The 'configure' script doesn't recognize things like
               ;; '--enable-fast-install'.
               (invoke "./configure"
                       (string-append "--build-prefix=" (getcwd) "/build")
                       (string-append "--prefix=" #$output)
                       (string-append "--debug")
                       (string-append "--with-fuse-prefix="
                                      #$(this-package-input "fuse"))
                       (string-append "--with-magic-prefix="
                                      #$(this-package-input "file"))
                       (string-append "--with-xml2-prefix="
                                      #$(this-package-input "libxml2"))
                       (string-append "--with-ncbi-vdb-sources="
                                      #$(this-package-input "ncbi-vdb"))
                       (string-append "--with-ncbi-vdb-build="
                                      #$(this-package-input "ncbi-vdb"))
                       (string-append "--with-ngs-sdk-prefix="
                                      #$(this-package-input "ngs-sdk"))
                       (string-append "--with-hdf5-prefix="
                                      #$(this-package-input "hdf5"))))))))
    (native-inputs (list perl))
    (inputs
     (list ngs-sdk
           ncbi-vdb
           file
           fuse-2
           hdf5-1.10
           libxml2
           zlib
           python-wrapper))
    (home-page
     "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
    (synopsis "Tools and libraries for reading and writing sequencing data")
    (description
     "The SRA Toolkit from NCBI is a collection of tools and libraries for
reading of sequencing files from the Sequence Read Archive (SRA) database and
writing files into the .sra format.")
    (license license:public-domain)))

(define-public seqan
  (package
    (name "seqan")
    (version "3.0.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/seqan/seqan3/releases/"
                                  "download/" version "/seqan3-"
                                  version "-Source.tar.xz"))
              (sha256
               (base32
                "1h2z0cvgidhkmh5xsbw75waqbrqbbv6kkrvb0b92xfh3gqpaiz22"))))
    (build-system cmake-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "ctest" "test" "--output-on-failure"))))))
    (native-inputs
     (list bzip2 cereal zlib))
    (home-page "https://www.seqan.de")
    (synopsis "Library for nucleotide sequence analysis")
    (description
     "SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data.  It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
    (license license:bsd-3)))

(define-public seqan-2
  (package
    (inherit seqan)
    (version "2.4.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/seqan/seqan/releases/"
                                  "download/seqan-v" version
                                  "/seqan-library-" version ".tar.xz"))
              (sha256
               (base32
                "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx"))))
    ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
    ;; makes sense to split the outputs.
    (outputs '("out" "doc"))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
       #:builder
       ,#~(begin
            (use-modules (guix build utils))
            (let ((tar #$(this-package-native-input "tar"))
                  (xz  #$(this-package-native-input "xz"))
                  (out #$output)
                  (doc #$output:doc))
              (setenv "PATH" (string-append tar "/bin:" xz "/bin"))
              (invoke "tar" "xvf" #$(this-package-native-input "source"))
              (chdir (string-append "seqan-library-" #$version))
              (copy-recursively "include" (string-append out "/include"))
              (copy-recursively "share"  (string-append doc "/share"))))))
    (native-inputs
     `(("source" ,source)
       ("tar" ,tar)
       ("xz" ,xz)))))

(define-public seqan-1
  (package (inherit seqan)
    (name "seqan")
    (version "1.4.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://packages.seqan.de/seqan-library/"
                                  "seqan-library-" version ".tar.bz2"))
              (sha256
               (base32
                "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
    ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
    ;; makes sense to split the outputs.
    (outputs '("out" "doc"))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
       #:builder
       ,#~(begin
            (use-modules (guix build utils))
            (let ((tar  #$(this-package-native-input "tar"))
                  (bzip #$(this-package-native-input "bzip2"))
                  (out #$output)
                  (doc #$output:doc))
              (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
              (invoke "tar" "xvf" #$(this-package-native-input "source"))
              (chdir (string-append "seqan-library-" #$version))
              (copy-recursively "include" (string-append out "/include"))
              (copy-recursively "share"  (string-append doc "/share"))))))
    (native-inputs
     `(("source" ,source)
       ("tar" ,tar)
       ("bzip2" ,bzip2)))))

(define-public seqmagick
  (package
    (name "seqmagick")
    (version "0.8.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "seqmagick" version))
       (sha256
        (base32
         "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0"))))
    (build-system pyproject-build-system)
    (inputs
     (list python-biopython python-pygtrie))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/fhcrc/seqmagick")
    (synopsis "Tools for converting and modifying sequence files")
    (description
     "Bioinformaticians often have to convert sequence files between formats
and do little manipulations on them, and it's not worth writing scripts for
that.  Seqmagick is a utility to expose the file format conversion in
BioPython in a convenient way.  Instead of having a big mess of scripts, there
is one that takes arguments.")
    (license license:gpl3)))

(define-public seqtk
  (package
    (name "seqtk")
    (version "1.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/lh3/seqtk")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'check
           ;; There are no tests, so we just run a sanity check.
           (lambda _ (invoke "./seqtk" "seq") #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
               (install-file "seqtk" bin)
               #t))))))
    (inputs
     (list zlib))
    (home-page "https://github.com/lh3/seqtk")
    (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
    (description
     "Seqtk is a fast and lightweight tool for processing sequences in the
FASTA or FASTQ format.  It parses both FASTA and FASTQ files which can be
optionally compressed by gzip.")
      (license license:expat)))

(define-public snap-aligner
  (package
    (name "snap-aligner")
    (version "2.0.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/amplab/snap")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0yag3jcazdqfxgmw0vbi91i98kj9sr0aqx83qqj6m5b45wxs7jms"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests? (invoke "./unit_tests"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin")))
               (install-file "snap-aligner" bin)
               (install-file "SNAPCommand" bin)))))))
    (native-inputs
     (list zlib))
    (home-page "https://snap.cs.berkeley.edu/")
    (synopsis "Short read DNA sequence aligner")
    (description
     "SNAP is a fast and accurate aligner for short DNA reads.  It is
optimized for modern read lengths of 100 bases or higher, and takes advantage
of these reads to align data quickly through a hash-based indexing scheme.")
    ;; 32-bit systems are not supported by the unpatched code.
    ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
    ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
    ;; systems without a lot of memory cannot make good use of this program.
    (supported-systems '("x86_64-linux"))
    (license license:asl2.0)))

(define-public sortmerna
  (package
    (name "sortmerna")
    (version "4.3.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/biocore/sortmerna")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0f8jfc8vsq6llhbb92p9yv7nbp566yqwfcmq3g2hw0n7d8hyl3a8"))))
    (build-system cmake-build-system)
    (outputs '("out"      ;for binaries
               "db"))     ;for sequence databases
    (arguments
     (list
      #:tests? #false ;unclear how to run them
      #:configure-flags
      #~(list "-DWITH_TESTS=ON"
              "-DCMAKE_CXX_FLAGS=-pthread"
              "-DZLIB_STATIC=OFF"
              "-DROCKSDB_STATIC=OFF"
              "-DPORTABLE=OFF" ;do not use static linking
              (string-append "-DROCKSDB_HOME="
                             #$(this-package-input "rocksdb"))
              (string-append "-DRAPIDJSON_HOME="
                             #$(this-package-input "rapidjson"))
              (string-append "-DRapidJson_DIR="
                             #$(this-package-input "rapidjson")
                             "/lib/cmake/RapidJSON")
              (string-append "-DRapidJSON_INCLUDE_DIR="
                             #$(this-package-input "rapidjson")
                             "/include"))
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'find-concurrentqueue-headers
           (lambda* (#:key inputs #:allow-other-keys)
             ;; Ensure that headers can be found
             (setenv "CPLUS_INCLUDE_PATH"
                     (string-append (search-input-directory
                                     inputs "/include/concurrentqueue")
                                    ":"
                                    (or (getenv "CPLUS_INCLUDE_PATH") "")))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out   (assoc-ref outputs "out"))
                    (bin   (string-append out "/bin"))
                    (db    (assoc-ref outputs "db"))
                    (share
                     (string-append db "/share/sortmerna/rRNA_databases")))
               (install-file "src/sortmerna" bin)
               (for-each (lambda (file)
                           (install-file file share))
                         (find-files "../source/data/rRNA_databases" ".*fasta"))))))))
    (inputs
     (list concurrentqueue
           gflags ; because of rocksdb
           rapidjson rocksdb zlib))
    (native-inputs
     (list pkg-config))
    (home-page "https://bioinfo.lifl.fr/RNA/sortmerna/")
    (synopsis "Biological sequence analysis tool for NGS reads")
    (description
     "SortMeRNA is a biological sequence analysis tool for filtering, mapping
and @acronym{OTU, operational taxonomic unit} picking of @acronym{NGS, next
generation sequencing} reads.  The core algorithm is based on approximate seeds
and allows for fast and sensitive analyses of nucleotide sequences.  The main
application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
    ;; The source includes x86 specific code
    (supported-systems '("x86_64-linux" "i686-linux"))
    (license license:lgpl3)))

(define-public star
  (package
    (name "star")
    (version "2.7.8a")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/alexdobin/STAR")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0zc5biymja9zml9yizcj1h68fq9c6sxfcav8a0lbgvgsm44rvans"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (substitute* "source/Makefile"
                    (("/bin/rm") "rm"))
                  ;; Remove pre-built binaries and bundled htslib sources.
                  (delete-file-recursively "bin/MacOSX_x86_64")
                  (delete-file-recursively "bin/Linux_x86_64")
                  (delete-file-recursively "bin/Linux_x86_64_static")
                  (delete-file-recursively "source/htslib")
                  #t))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no check target
       #:make-flags '("STAR")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-source-dir
           (lambda _ (chdir "source") #t))
         (add-after 'enter-source-dir 'make-reproducible
           (lambda _
             (substitute* "Makefile"
               (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
                (string-append pre "Built with Guix" post)))
             #t))
         ;; See https://github.com/alexdobin/STAR/pull/562
         (add-after 'enter-source-dir 'add-missing-header
           (lambda _
             (substitute* "SoloReadFeature_inputRecords.cpp"
               (("#include \"binarySearch2.h\"" h)
                (string-append h "\n#include <math.h>")))
             #t))
         (add-after 'enter-source-dir 'do-not-use-bundled-htslib
           (lambda _
             (substitute* "Makefile"
               (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
                 _ prefix) prefix))
             (substitute* '("BAMfunctions.cpp"
                            "signalFromBAM.h"
                            "bam_cat.h"
                            "bam_cat.c"
                            "STAR.cpp"
                            "bamRemoveDuplicates.cpp")
               (("#include \"htslib/([^\"]+\\.h)\"" _ header)
                (string-append "#include <" header ">")))
             (substitute* "IncludeDefine.h"
               (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
                (string-append "<" header ">")))
             #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
               (install-file "STAR" bin))
             #t))
         (delete 'configure))))
    (native-inputs
     (list xxd))
    (inputs
     (list htslib zlib))
    (home-page "https://github.com/alexdobin/STAR")
    (synopsis "Universal RNA-seq aligner")
    (description
     "The Spliced Transcripts Alignment to a Reference (STAR) software is
based on a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays followed
by seed clustering and stitching procedure.  In addition to unbiased de novo
detection of canonical junctions, STAR can discover non-canonical splices and
chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
sequences.")
    ;; Only 64-bit systems are supported according to the README.
    (supported-systems '("x86_64-linux" "mips64el-linux"))
    ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
    (license license:gpl3+)))

(define-public star-for-pigx
  (package
    (inherit star)
    (name "star")
    (version "2.7.3a")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/alexdobin/STAR")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (substitute* "source/Makefile"
                    (("/bin/rm") "rm"))
                  ;; Remove pre-built binaries and bundled htslib sources.
                  (delete-file-recursively "bin/MacOSX_x86_64")
                  (delete-file-recursively "bin/Linux_x86_64")
                  (delete-file-recursively "bin/Linux_x86_64_static")
                  (delete-file-recursively "source/htslib")
                  #t))))))

(define-public starlong
  (package (inherit star)
    (name "starlong")
    (arguments
     (substitute-keyword-arguments (package-arguments star)
       ((#:make-flags flags)
        `(list "STARlong"))
       ((#:phases phases)
        `(modify-phases ,phases
           ;; Allow extra long sequence reads.
           (add-after 'unpack 'make-extra-long
             (lambda _
               (substitute* "source/IncludeDefine.h"
                 (("(#define DEF_readNameLengthMax ).*" _ match)
                  (string-append match "900000\n")))
               #t))
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
                 (install-file "STARlong" bin))
               #t))))))))

(define-public subread
  (package
    (name "subread")
    (version "2.0.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/subread/subread-"
                                  version "/subread-" version "-source.tar.gz"))
              (sha256
               (base32
                "0szmllia7jl0annk5568xjhw6cc8yj1c5mb961qk5m0lz6ig7kjn"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
      ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
      ;; optimizations by default, so we override these flags such that x86_64
      ;; flags are only added when the build target is an x86_64 system.
       #:make-flags
       (list (let ((system ,(or (%current-target-system)
                                (%current-system)))
                   (flags '("-ggdb" "-fomit-frame-pointer"
                            "-ffast-math" "-funroll-loops"
                            "-fmessage-length=0" "-fcommon"
                            "-O9" "-Wall" "-DMAKE_FOR_EXON"
                            "-DMAKE_STANDALONE"
                            "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
                   (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
               (if (string-prefix? "x86_64" system)
                   (string-append "CCFLAGS=" (string-join (append flags flags64)))
                   (string-append "CCFLAGS=" (string-join flags))))
             "-f" "Makefile.Linux"
             "CC=gcc ${CCFLAGS}")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-dir
           (lambda _ (chdir "src")))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
               (mkdir-p bin)
               (copy-recursively "../bin" bin))))
         ;; no "configure" script
         (delete 'configure))))
    (inputs (list zlib))
    (home-page "https://subread.sourceforge.net/")
    (synopsis "Tool kit for processing next-gen sequencing data")
    (description
     "The subread package contains the following tools: subread aligner, a
general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
features; exactSNP: a SNP caller that discovers SNPs by testing signals
against local background noises.")
    (license license:gpl3+)))

(define-public stringtie
  (package
    (name "stringtie")
    (version "2.2.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
                                  "stringtie-" version ".tar.gz"))
              (sha256
               (base32
                "08w3ish4y9kf9acp7k38iwi8ixa6j51m6qyf0vvfj7yz78a3ai3x"))
              ;; This package bundles an annoying amount of third party source
              ;; code.
              (modules '((guix build utils)))
              (snippet
               '(delete-file-recursively "htslib"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no test suite
       #:make-flags '("LIBDEFLATE=-ldeflate"
                      "LIBBZ2=-lbz2"
                      "LIBLZMA=-llzma")
       #:phases
       (modify-phases %standard-phases
         ;; no configure script
         (delete 'configure)
         (add-before 'build 'use-system-samtools
           (lambda _
             (substitute* "Makefile"
               ((" -lm") " -lm -lhts")
               ((" \\$\\{HTSLIB\\}/libhts\\.a") " "))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
               (install-file "stringtie" bin)))))))
    (inputs
     (list bzip2 htslib-for-stringtie libdeflate zlib))
    (home-page "https://ccb.jhu.edu/software/stringtie/")
    (synopsis "Transcript assembly and quantification for RNA-Seq data")
    (description
     "StringTie is a fast and efficient assembler of RNA-Seq sequence
alignments into potential transcripts.  It uses a novel network flow algorithm
as well as an optional de novo assembly step to assemble and quantitate
full-length transcripts representing multiple splice variants for each gene
locus.  Its input can include not only the alignments of raw reads used by
other transcript assemblers, but also alignments of longer sequences that have
been assembled from those reads.  To identify differentially expressed genes
between experiments, StringTie's output can be processed either by the
Cuffdiff or Ballgown programs.")
    (license license:expat)))

(define-public taxtastic
  (package
    (name "taxtastic")
    (version "0.9.2")
    (source (origin
              ;; The Pypi version does not include tests.
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/fhcrc/taxtastic")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'prepare-directory
           (lambda _
             ;; This test fails, but the error is not caught by the test
             ;; framework, so the tests fail...
             (substitute* "tests/test_taxit.py"
               (("self.cmd_fails\\(''\\)")
                "self.cmd_fails('nothing')"))
             ;; This version file is expected to be created with git describe.
             (mkdir-p "taxtastic/data")
             (with-output-to-file "taxtastic/data/ver"
               (lambda () (display ,version)))))
         (replace 'check
           ;; Note, this fails to run with "-v" as it tries to write to a
           ;; closed output stream.
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "python" "-m" "unittest"))))
         ;; This fails because it cannot find psycopg2 even though it is
         ;; available.
         (delete 'sanity-check))))
    (propagated-inputs
     (list python-sqlalchemy
           python-decorator
           python-biopython
           python-pandas
           python-psycopg2
           python-fastalite
           python-pyyaml
           python-six
           python-jinja2
           python-dendropy))
    (home-page "https://github.com/fhcrc/taxtastic")
    (synopsis "Tools for taxonomic naming and annotation")
    (description
     "Taxtastic is software written in python used to build and maintain
reference packages i.e. collections of reference trees, reference alignments,
profiles, and associated taxonomic information.")
    (license license:gpl3+)))

(define-public vcftools
  (package
    (name "vcftools")
    (version "0.1.16")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/vcftools/vcftools/releases/download/v"
                    version "/vcftools-" version ".tar.gz"))
              (sha256
               (base32
                "1qqlx7flfv7axrjwkaz6njkscsl1d0jw98ns8d8bh1n1hd1pgz6v"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; no "check" target
       #:make-flags
       ,#~(list
           "CFLAGS=-O2"                 ; override "-m64" flag
           (string-append "PREFIX=" #$output)
           (string-append "MANDIR=" #$output "/share/man/man1"))))
    (native-inputs
     (list pkg-config))
    (inputs
     (list perl zlib))
    (home-page "https://vcftools.github.io/")
    (synopsis "Tools for working with VCF files")
    (description
     "VCFtools is a program package designed for working with VCF files, such
as those generated by the 1000 Genomes Project.  The aim of VCFtools is to
provide easily accessible methods for working with complex genetic variation
data in the form of VCF files.")
    ;; The license is declared as LGPLv3 in the README and
    ;; at https://vcftools.github.io/license.html
    (license license:lgpl3)))

(define-public infernal
  (package
    (name "infernal")
    (version "1.1.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://eddylab.org/software/infernal/"
                                  "infernal-" version ".tar.gz"))
              (sha256
               (base32
                "1z4mgwqg1j4n5ika08ai8mg9yjyjhf4821jp83v2bgwzxrykqjgr"))))
    (build-system gnu-build-system)
    (native-inputs
     (list perl python)) ; for tests
    (home-page "http://eddylab.org/infernal/")
    (synopsis "Inference of RNA alignments")
    (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
searching DNA sequence databases for RNA structure and sequence similarities.
It is an implementation of a special case of profile stochastic context-free
grammars called @dfn{covariance models} (CMs).  A CM is like a sequence
profile, but it scores a combination of sequence consensus and RNA secondary
structure consensus, so in many cases, it is more capable of identifying RNA
homologs that conserve their secondary structure more than their primary
sequence.")
    ;; Infernal 1.1.3 requires VMX or SSE capability for parallel instructions.
    (supported-systems '("i686-linux" "x86_64-linux"))
    (license license:bsd-3)))

(define-public r-ggexpress
  (let ((commit "82f169385f87af328ff971195c2f64ff3c573a8a")
        (revision "1"))
    (package
      (name "r-ggexpress")
      (version (git-version "0.6.6" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/ggExpress")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "122hnw8xv33ngcd4fd7hmf817a06ih1knrxxi0cgklj1fwinm0z4"))))
      (properties `((upstream-name . "ggExpress")))
      (build-system r-build-system)
      (propagated-inputs (list r-cowplot
                               r-ggplot2
                               r-ggpubr
                               r-markdownhelpers
                               r-markdownreports
                               r-rcolorbrewer
                               r-sessioninfo
                               r-seurat
                               r-sm
                               r-stringendo
                               r-tidyverse))
      (home-page "https://github.com/vertesy/ggExpress")
      (synopsis
       "This is a fast tool to create, annotate and export plots in R")
      (description
       "This package is a set of R functions for generating precise figures.
This tool helps you to create clean markdown reports about what you just
discovered with your analysis script.")
      (license license:gpl3))))

(define-public r-gg3d
  (let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0")
        (revision "1"))
    (package
      (name "r-gg3d")
      (version (git-version "0.0.0.9000" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/AckerDWM/gg3D")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0vz5laj5vz9m1jzb7h7q9f37zjmxwhylhaidlsg61r57wpxvjr3p"))))
      (properties `((upstream-name . "gg3D")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-dplyr
             r-ggplot2
             r-magrittr
             r-plot3d
             r-plyr
             r-scales))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/AckerDWM/gg3D")
      (synopsis "3D perspective plots for ggplot2")
      (description
       "This package adds 3D perspective plotting of points, paths, and line,
3D perspective axes, 3D perspective annotations, and wireframe plots.")
      (license license:gpl3+))))

(define-public r-ggsankey
  (let ((commit "be08dd0f86eaee9f9ff9e7ff95d47930660a3c36")
        (revision "1"))
    (package
      (name "r-ggsankey")
      (version (git-version "0.0.99999" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/davidsjoberg/ggsankey")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0acpmydqqc91pq5p9wpkpmgqp3nhiljabd7d3i00kwhjxgm2bvba"))))
      (properties `((upstream-name . "ggsankey")))
      (build-system r-build-system)
      (propagated-inputs (list r-dplyr
                               r-ggplot2
                               r-magrittr
                               r-purrr
                               r-stringr
                               r-tidyr))
      (home-page "https://github.com/davidsjoberg/ggsankey")
      (synopsis "Sankey, Alluvial and Sankey bump plots")
      (description
       "This package provides a package that makes it easy to implement
sankey, alluvial and sankey bump plots in @code{ggplot2}.")
      (license license:expat))))

(define-public r-gutils
  (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6")
        (revision "1"))
    (package
      (name "r-gutils")
      (version (git-version "0.2.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/mskilab/gUtils")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1wq9kd1afzy7ii510r20c4n9fkykj6p15q5c85ws27h1q5w4ghxy"))))
      (properties `((upstream-name . "gUtils")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocgenerics
             r-data-table
             r-genomeinfodb
             r-genomicranges
             r-iranges
             r-matrix
             r-s4vectors
             r-stringr))
      (home-page "https://github.com/mskilab/gUtils")
      (synopsis "Additional capabilities and speed for GenomicRanges operations")
      (description
       "This is an R package providing additional capabilities and speed for
@code{GenomicRanges} operations.")
      (license license:gpl2))))

(define-public r-bamutils
  (let ((commit "639dba901f16944fa1b7a8d7048701ba86a2cdb8")
        (revision "1"))
    (package
      (name "r-bamutils")
      (version (git-version "0.0.0.9000" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/mskilab/bamutils/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0qwby2v5rydnipvf1iv1wz9nf02yq98k0xbc4inf9mqc54jwacs0"))))
      (properties `((upstream-name . "bamUtils")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-abind
             r-biocgenerics
             r-data-table
             r-genomicalignments
             r-genomicranges
             r-gutils
             r-rsamtools
             r-variantannotation))
      (home-page "https://github.com/mskilab/bamutils/")
      (synopsis "Utility functions for manipulating BAMs")
      (description "This package provides utility functions for manipulating
BAM files.")
      (license license:gpl2))))

(define-public r-gtrack
  (let ((commit "a694fa36cedafca2658da79fc8e5b673535b15e5")
        (revision "1"))
    (package
      (name "r-gtrack")
      (version (git-version "0.1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/mskilab/gTrack/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "070qlrbqsbj9max2vx740zigqh0ymvnw2pm1ia5la3wb4dbfwh2b"))))
      (properties `((upstream-name . "gTrack")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocgenerics
             r-data-table
             r-genomeinfodb
             r-genomicranges
             r-gutils
             r-iranges
             r-matrix
             r-rcolorbrewer
             r-rcpp
             r-rcurl
             r-rtracklayer
             r-s4vectors))
      (home-page "https://github.com/mskilab/gTrack/")
      (synopsis "Plot tracks of complex genomic data across multiple genomic windows")
      (description
       "This package provides an object for plotting GRanges, RleList, UCSC
file formats, and ffTrack objects in multi-track panels.")
      (license license:gpl2))))

(define-public r-gchain
  (let ((commit "dc393e8dd0d8efaf36270c04d7112db8553db36a")
        (revision "1"))
    (package
      (name "r-gchain")
      (version (git-version "0.2.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/mskilab/gChain/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "105wgi5w2fhwq1grsvj6zjigwg0sny3z7zr577q8ki3qffjwdkj0"))))
      (properties `((upstream-name . "gChain")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-bamutils
             r-biostrings
             r-data-table
             r-genomicalignments
             r-genomicranges
             r-gtrack
             r-gutils
             r-matrix
             r-rtracklayer))
      (home-page "https://github.com/mskilab/gChain/")
      (synopsis "Additional capabilities and speed for GenomicRanges operations")
      (description
       "This R package provides additional capabilities and speed for
GenomicRanges operations.")
      (license license:gpl2))))

(define-public r-skitools
  (let ((commit "22d107d32f063eb891eb5e7fb36996d1c0b0d2bc")
        (revision "1"))
    (package
      (name "r-skitools")
      (version (git-version "0.0.0.9000" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/mskilab/skitools/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1977d9bkdk9l2n6niahfj9vksh9l1ga4g7c3b3x27lj1gc0qgr4z"))))
      (properties `((upstream-name . "skitools")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biostrings
             r-complexheatmap
             r-data-table
             r-devtools
             r-dt
             r-gchain
             r-genomeinfodb
             r-genomicranges
             r-ggplot2
             r-gplots
             r-gutils
             r-htmlwidgets
             r-hwriter
             r-igraph
             r-iranges
             r-plotly
             r-rcolorbrewer
             r-reshape2
             r-s4vectors
             r-stringr
             r-variantannotation))
      (home-page "https://github.com/mskilab/skitools/")
      (synopsis "Various mskilab R utilities")
      (description
       "This package provides R miscellaneous utilities for basic data
manipulation, debugging, visualization, lsf management, and common mskilab
tasks.")
      (license license:expat))))

(define-public r-chromunity
  (let ((commit "712e56ccba64e8881dbb203546379a5c3c639bb2")
        (revision "1"))
    (package
      (name "r-chromunity")
      (version (git-version "0.0.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/mskilab/chromunity")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0sdja11l7bg5rmcbp2cl226cq9qrj3r8kq5lg49zbin83hya27vh"))))
      (properties `((upstream-name . "chromunity")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-arrow
             r-biocgenerics
             r-bsgenome-hsapiens-ucsc-hg38
             r-data-table
             r-gchain
             r-genomicranges
             r-gutils
             r-igraph
             r-magrittr
             r-mass
             r-matrix
             r-pbmcapply
             r-plyr
             r-r6
             r-zoo))
      (home-page "https://github.com/mskilab/chromunity")
      (synopsis "Discovery of communities in Pore-C concatemers")
      (description "This is a package for the discovery of communities in
Pore-C concatemers.")
      (license license:gpl3))))

(define-public r-cmdstanr
  (let ((commit "a45d4f7d686aa6b57ce25f342a71eea79507f01c")
        (revision "1"))
    (package
      (name "r-cmdstanr")
      (version (git-version "0.8.1.9000" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/stan-dev/cmdstanr")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "01vyh3sy704rs7yvaka2hp6vld0mdl7hbrs20dpbwidgm4ksrvsi"))))
      (properties `((upstream-name . "cmdstanr")))
      (build-system r-build-system)
      (propagated-inputs (list r-checkmate
                               r-data-table
                               r-jsonlite
                               r-posterior
                               r-processx
                               r-r6
                               r-rlang
                               r-withr))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/stan-dev/cmdstanr")
      (synopsis "R interface to 'CmdStan'")
      (description
       "This package provides a lightweight interface to Stan
<https://mc-stan.org>.  The @code{CmdStanR} interface is an alternative
to RStan that calls the command line interface for compilation and
running algorithms instead of interfacing with C++ via Rcpp'.")
      (license license:bsd-3))))

(define-public r-dnamcrosshyb
  ;; There aren't any releases.
  (let ((commit "fe8acb33667e81f00dcb84e0fa75c87ab2db5d8f")
        (revision "1"))
    (package
      (name "r-dnamcrosshyb")
      (version (git-version "0.0.0.9000" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/pjhop/DNAmCrosshyb")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "12j1xsiqpvny5rp23z1az0k4cj5ajbcwkg65z00s16vywi2rx6nb"))))
      (properties `((upstream-name . "DNAmCrosshyb")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocgenerics
             r-biocparallel
             r-biostrings
             r-bsgenome-hsapiens-ucsc-hg19-masked
             r-bsgenome-hsapiens-ucsc-hg38-masked
             r-dplyr
             r-genomicranges
             r-ggplot2
             r-iranges
             r-magrittr
             r-minfi
             r-purrr
             r-s4vectors
             r-shiny
             r-stringi
             r-stringr
             r-tibble
             r-tidyr
             r-watermelon))
      (home-page "https://github.com/pjhop/DNAmCrosshyb")
      (synopsis "DNAmCrosshyb")
      (description
       "This package provides helper functions to detect cross-hybridization
on Illumina DNAm arrays.")
      (license license:gpl3))))

(define-public r-doubletcollection
  (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd")
        (revision "1"))
    (package
      (name "r-doubletcollection")
      (version (git-version "1.1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/xnnba1984/DoubletCollection")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "02cvibyc2nwc4037ramm5cskjwyrb9ib9hkrfhmvhbslkn5ixz1v"))))
      (properties `((upstream-name . "DoubletCollection")))
      (build-system r-build-system)
      (propagated-inputs (list r-biocgenerics
                               r-doubletfinder
                               r-gam
                               r-ggplot2
                               r-ggthemes
                               r-mast
                               r-mclust
                               r-prroc
                               r-reticulate
                               r-scales
                               r-scdblfinder
                               r-scds
                               r-seurat
                               r-singlecellexperiment
                               r-slingshot
                               r-summarizedexperiment
                               python
                               python-scrublet
                               python-doubletdetection))
      (home-page "https://github.com/xnnba1984/DoubletCollection")
      (synopsis "Tool for finding doublets in scRNA-seq data")
      (description
       "This is an R package that integrates the installation of
doublet-detection methods.  In addition, this tool is used for execution and
benchmark of those eight mentioned methods.")
      (license license:gpl3+))))

(define-public r-plsdabatch
  (let ((commit "4aadf3a99709afae462db310386b6cf5db20088c")
        (revision "1"))
    (package
      (name "r-plsdabatch")
      (version (git-version "0.2.3" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/EvaYiwenWang/PLSDAbatch")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "047l923lq2ji7rwybh9b9zkblzvvhkpli5gb2x8g2q9f2n5022nr"))))
      (properties `((upstream-name . "PLSDAbatch")))
      (build-system r-build-system)
      (propagated-inputs (list r-ggplot2
                               r-ggpubr
                               r-gridextra
                               r-lmertest
                               r-mixomics
                               r-mvtnorm
                               r-performance
                               r-rdpack
                               r-scales))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/EvaYiwenWang/PLSDAbatch")
      (synopsis "PLSDA-batch")
      (description
       "This package provides a new batch effect correction method based on
Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to
correct data prior to any downstream analysis.  PLSDA-batch estimates latent
components related to treatment and batch effects to remove batch variation.
The method is multivariate, non-parametric and performs dimension reduction.
Combined with centered log ratio transformation for addressing uneven library
sizes and compositional structure, PLSDA-batch addresses all characteristics
of microbiome data that existing correction methods have ignored so far.")
      (license license:gpl3))))

(define-public r-psupertime
  (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207")
        (revision "1"))
    (package
      (name "r-psupertime")
      (version (git-version "0.2.6" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/wmacnair/psupertime")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "00h1r3ffz6m9dwcgkvyki8405b059qn6mnjsd8d76a1rabaf2vfh"))))
      (properties `((upstream-name . "psupertime")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-cowplot
             r-data-table
             r-fastcluster
             r-forcats
             r-ggplot2
             r-glmnet
             r-knitr
             r-matrix
             r-rcolorbrewer
             r-scales
             r-scran
             r-singlecellexperiment
             r-stringr
             r-summarizedexperiment
             r-topgo))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/wmacnair/psupertime")
      (synopsis
       "Psupertime is supervised pseudotime for single cell RNAseq data")
      (description
       "Psupertime is supervised pseudotime for single cell RNAseq data.  It
uses single cell RNAseq data, where the cells have a known ordering.  This
ordering helps to identify a small number of genes which place cells in that
known order.  It can be used for discovery of relevant genes, for
identification of subpopulations, and characterization of further unknown or
differently labelled data.")
      (license license:gpl3))))

(define-public r-pando
  (package
    (name "r-pando")
    (version "1.0.5")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/quadbiolab/Pando")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "04kr1b28p5j7h48g32cldkg87xcmxnmd4kspygkfs7a4amihpi66"))))
    (properties `((upstream-name . "Pando")))
    (build-system r-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'loosen-requirements
           (lambda _
             (substitute* "DESCRIPTION"
               ((" \\(==.*,") ",")))))))
    (propagated-inputs
     (list r-bayestestr
           r-foreach
           r-genomicranges
           r-ggplot2
           r-ggpointdensity
           r-ggraph
           r-glmnetutils
           r-grr
           r-iranges
           r-irlba
           r-matrix
           r-matrixgenerics
           r-motifmatchr
           r-pals
           r-patchwork
           r-seurat
           r-signac
           r-sparsematrixstats
           r-tfbstools
           r-tidygraph
           r-tidyverse
           r-uwot))
    (native-inputs (list r-knitr))
    (home-page "https://github.com/quadbiolab/Pando")
    (synopsis "Infer regulomes from multi-modal single-cell genomics data")
    (description
     "Pando leverages multi-modal single-cell measurements to infer gene
regulatory networks using a flexible linear model-based framework.  By
modeling the relationship between TF-binding site pairs with the expression of
target genes, Pando simultaneously infers gene modules and sets of regulatory
regions for each transcription factor.")
    (license license:expat)))

(define-public r-premessa
  (let ((commit "68b42bb984637d0f3ad6a0ecc83e9278994afc85")
        (revision "1"))
    (package
      (name "r-premessa")
      (version (git-version "0.3.4" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/ParkerICI/premessa")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1l0q431zk0lvg22130nx84gdqi7cpl05yah4am63lbx6m4c769pb"))
                (snippet
                 '(delete-file "inst/normalizer_shinyGUI/www/d3.min.js"))))
      (properties `((upstream-name . "premessa")))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'process-javascript
             (lambda* (#:key inputs #:allow-other-keys)
               (with-directory-excursion "inst/normalizer_shinyGUI/www/"
                 (invoke "esbuild" (assoc-ref inputs "d3.v4.js")
                         "--minify" "--outfile=d3.min.js")))))))
      (propagated-inputs
       (list r-data-table
             r-flowcore
             r-ggplot2
             r-gridextra
             r-hexbin
             r-jsonlite
             r-reshape
             r-rhandsontable
             r-shiny
             r-shinyjqui))
      (native-inputs
       `(("esbuild" ,esbuild)
         ("d3.v4.js"
          ,(origin
             (method url-fetch)
             (uri "https://d3js.org/d3.v4.js")
             (sha256
              (base32
               "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
      (home-page "https://github.com/ParkerICI/premessa")
      (synopsis "Pre-processing of flow and mass cytometry data")
      (description
       "This is an R package for pre-processing of flow and mass cytometry
data.  This package includes panel editing or renaming for FCS files,
bead-based normalization and debarcoding.")
      (license license:gpl3))))

(define-public r-projectils
  (let ((commit "cc73b97471b4b6eea11ce779b5c4a7dc5c3e1709")
        (revision "1"))
    (package
      (name "r-projectils")
      (version (git-version "3.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/carmonalab/ProjecTILs")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0dpzvbhhb9andnj7angpj32cgkwd6rs6qgpl6i21pqzcn6vqqhqw"))))
      (properties `((upstream-name . "ProjecTILs")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocneighbors
             r-biocparallel
             r-dplyr
             r-ggplot2
             r-matrix
             r-patchwork
             r-pheatmap
             r-pracma
             r-purrr
             r-rcolorbrewer
             r-reshape2
             r-scales
             r-scgate
             r-seurat
             r-seuratobject
             r-stacas
             r-ucell
             r-umap
             r-uwot))
      (home-page "https://github.com/carmonalab/ProjecTILs")
      (synopsis "Reference-based analysis of scRNA-seq data")
      (description
       "This package implements methods to project single-cell RNA-seq data
onto a reference atlas, enabling interpretation of unknown cell transcriptomic
states in the the context of known, reference states.")
      (license license:gpl3))))

(define-public r-presto
  (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
        (revision "0"))
    (package
      (name "r-presto")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/immunogenomics/presto")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1c3fmag4r4p2lvbvxlxyck9dvfw1prbwcl9665mmlx4a35750hk8"))))
      (properties `((upstream . "presto")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-data-table
             r-deseq2
             r-dplyr
             r-matrix
             r-rcpp
             r-rcpparmadillo
             r-reshape2
             r-rlang
             r-tidyr))
      (home-page "https://github.com/immunogenomics/presto")
      (synopsis "Fast Functions for Differential Expression using Wilcox and AUC")
      (description "This package performs a fast Wilcoxon rank sum test and
auROC analysis.")
      (license license:gpl3))))

(define-public r-sccustomize
  (let ((commit "397374590dae2ccc0c560897dcd1ce4382c18798")
        (revision "1"))
    (package
      (name "r-sccustomize")
      (version (git-version "2.0.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/samuel-marsh/scCustomize")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "11bafm0mlck27fqd8brz80pxb8dc5q0aqbp8zv0s9sx97njp7wsl"))))
      (properties `((upstream-name . "scCustomize")))
      (build-system r-build-system)
      (propagated-inputs (list r-circlize
                               r-colorway
                               r-cowplot
                               r-data-table
                               r-dittoseq
                               r-dplyr
                               r-forcats
                               r-ggbeeswarm
                               r-ggplot2
                               r-ggprism
                               r-ggpubr
                               r-ggrastr
                               r-ggrepel
                               r-glue
                               r-janitor
                               r-magrittr
                               r-matrix
                               r-paletteer
                               r-patchwork
                               r-pbapply
                               r-purrr
                               r-remotes
                               r-scales
                               r-scattermore
                               r-seurat
                               r-seuratobject
                               r-stringi
                               r-stringr
                               r-tibble
                               r-tidyr
                               r-tidyselect
                               r-viridis))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/samuel-marsh/scCustomize")
      (synopsis "Custom visualization and analyses of single-cell sequencing")
      (description
       "This is a collection of functions created and/or curated to aid in the
visualization and analysis of single-cell data using R.")
      (license license:gpl3+))))

(define-public r-markdownhelpers
  (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe")
        (revision "1"))
    (package
      (name "r-markdownhelpers")
      (version (git-version "0.2.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/MarkdownHelpers")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1d18s2ydhfjm3hjkxz42dirhwrrv792m6mvkmypallaa2qnwrmkg"))))
      (properties `((upstream-name . "MarkdownHelpers")))
      (build-system r-build-system)
      (propagated-inputs (list r-devtools r-stringendo r-usethis))
      (home-page "https://github.com/vertesy/MarkdownHelpers")
      (synopsis "Helper functions for MarkdownReports and ggExpress")
      (description
       "This package provides a set of R functions to parse markdown and other
generic helpers.")
      (license license:gpl3))))

(define-public r-markdownreports
  (let ((commit "3ba1103e3ddc6df3a0c090eb884f5e65c461eb31")
        (revision "1"))
    (package
      (name "r-markdownreports")
      (version (git-version "4.5.9" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/MarkdownReports")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1xmasdb630b6nvxi5m1i8pyxiy49nxpzyxf9h8spdppx92rhdkc8"))))
      (properties `((upstream-name . "MarkdownReports")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-clipr
             r-codeandroll2
             r-colorramps
             r-devtools
             r-gplots
             r-markdownhelpers
             r-rcolorbrewer
             r-readwriter
             r-sessioninfo
             r-sm
             r-stringendo
             r-venndiagram
             r-vioplot))
      (home-page "https://github.com/vertesy/MarkdownReports")
      (synopsis "Tool for generating cientific figures and reports")
      (description
       "This is a set of R functions that allows you to generate precise
figures.  This tool will create clean markdown reports about what you just
discovered.")
      (license license:gpl3))))

(define-public r-metacell
  (let ((commit "d6a6926d103ee0cb34a611c753572429c94a53d9")
        (revision "1"))
    (package
      (name "r-metacell")
      (version (git-version "0.3.41" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/tanaylab/metacell/")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0zrsckr3y35x37mj3ibm6scyqx925s84wzrz1i42fnm9n3msc265"))))
      (properties `((upstream-name . "metacell")))
      (build-system r-build-system)
      (propagated-inputs (list r-cluster
                               r-cowplot
                               r-data-table
                               r-dbscan
                               r-domc
                               r-dplyr
                               r-entropy
                               r-ggplot2
                               r-graph
                               r-igraph
                               r-kernsmooth
                               r-magrittr
                               r-matrix
                               r-matrixstats
                               r-pdist
                               r-pheatmap
                               r-plyr
                               r-rcolorbrewer
                               r-rcurl
                               r-rgraphviz
                               r-slam
                               r-singlecellexperiment
                               r-svglite
                               r-tgconfig
                               r-tgstat
                               r-tgutil
                               r-tidyr
                               r-umap
                               r-umap
                               r-zoo))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/tanaylab/metacell/")
      (synopsis "Meta cell analysis for single cell RNA-seq data")
      (description
       "This package facilitates the analysis of single-cell RNA-seq UMI matrices.
It does this by computing partitions of a cell similarity graph into
small homogeneous groups of cells, which are defined as metacells (MCs).
The derived MCs are then used for building different representations of
the data, allowing matrix or 2D graph visualization forming a basis for
analysis of cell types, subtypes, transcriptional gradients,cell-cycle
variation, gene modules and their regulatory models and more.")
      (license license:expat))))

(define-public r-metadeconfoundr
  ;; There are some relevant updates after the release of version 0.3.0.
  (let ((commit "90aec0226c5128bfcbbc08903452eff460d21424")
        (revision "1"))
    (package
      (name "r-metadeconfoundr")
      (version (git-version "0.3.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/TillBirkner/metadeconfoundR")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0zkqar27p5qwq46xbxsw5x1pl50xbkgqiizw5bydlyhwb0ga2f3h"))))
      (properties `((upstream-name . "metadeconfoundR")))
      (build-system r-build-system)
      (propagated-inputs (list r-bigmemory
                               r-detectseparation
                               r-doparallel
                               r-dosnow
                               r-foreach
                               r-futile-logger
                               r-ggplot2
                               r-lme4
                               r-lmtest
                               r-reshape2
                               r-snow))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/TillBirkner/metadeconfoundR")
      (synopsis "Check multiple covariates for potenial confounding effects")
      (description
       "This package detects naive associations between omics features and
metadata in cross-sectional data-sets using non-parametric tests.  In a second
step, confounding effects between metadata associated to the same omics
feature are detected and labeled using nested post-hoc model comparison tests.
The generated output can be graphically summarized using the built-in plotting
function.")
      (license license:gpl2))))

(define-public r-sleuth
  (package
    (name "r-sleuth")
    (version "0.30.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/pachterlab/sleuth")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "09xgc7r6iisjkk0c0wn0q56zy0aph386kphwixfzq4422y7vlqci"))))
    (properties `((upstream-name . "sleuth")))
    (build-system r-build-system)
    (propagated-inputs (list r-aggregation
                             r-data-table
                             r-dplyr
                             r-ggplot2
                             r-lazyeval
                             r-matrixstats
                             r-pheatmap
                             r-reshape2
                             r-rhdf5
                             r-shiny
                             r-tidyr))
    (native-inputs (list r-knitr))
    (home-page "https://github.com/pachterlab/sleuth")
    (synopsis "Tools for investigating RNA-Seq")
    (description
     "Sleuth is a program for differential analysis of RNA-Seq data.
It makes use of quantification uncertainty estimates obtained via Kallisto for
accurate differential analysis of isoforms or genes, allows testing in the
context of experiments with complex designs, and supports interactive
exploratory data analysis via sleuth live.")
    (license license:gpl3)))

(define-public r-snapatac
  (package
    (name "r-snapatac")
    (version "2.0")
    (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/r3fang/SnapATAC")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
          (base32 "037jzlbl436fi7lkpq7d83i2vd1crnrik3vac2x6xj75dbikb2av"))))
    (properties `((upstream-name . "SnapATAC")))
    (build-system r-build-system)
    (propagated-inputs
      (list r-bigmemory
            r-doparallel
            r-dosnow
            r-edger
            r-foreach
            r-genomicranges
            r-igraph
            r-iranges
            r-irlba
            r-matrix
            r-plyr
            r-plot3d
            r-rann
            r-raster
            r-rcolorbrewer
            r-rhdf5
            r-rtsne
            r-scales
            r-viridis))
    (home-page "https://github.com/r3fang/SnapATAC")
    (synopsis "Single nucleus analysis package for ATAC-Seq")
    (description
      "This package provides a fast and accurate analysis toolkit for single
cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing).
Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and
reveal cell-type specific regulatory landscapes.  However, the exceeding data
sparsity has posed unique challenges for the data analysis.  This package
@code{r-snapatac} is an end-to-end bioinformatics pipeline for analyzing large-
scale single cell ATAC-seq data which includes quality control, normalization,
clustering analysis, differential analysis, motif inference and exploration of
single cell ATAC-seq sequencing data.")
    (license license:gpl3)))

(define-public r-tsis
  (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc")
        (revision "1"))
    (package
      (name "r-tsis")
      (version (git-version "0.2.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/wyguo/TSIS")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "17c8i25iwhldvs3c51m0wny40iffm8szzijalpwrxhzbv0xa94rb"))))
      (properties `((upstream-name . "TSIS")))
      (build-system r-build-system)
      (native-inputs (list r-knitr))
      (home-page "https://github.com/wyguo/TSIS")
      (synopsis "Time-series isoform switch of alternative splicing")
      (description
       "TSIS is used for detecting transcript isoform switches in time-series
data.  Transcript isoform switches occur when a pair of alternatively spliced
isoforms reverse the order of their relative expression levels.  TSIS
characterizes the transcript switch by defining the isoform switch time-points
for any pair of transcript isoforms within a gene.  In addition, this tool
describes the switch using five different features or metrics.  Also it
filters the results with user’s specifications and visualizes the results
using different plots for the user to examine further details of the
switches.")
      (license license:gpl3))))

(define-public r-umi4cpackage
  (let ((commit "88b07d896a137418ba6c31c2474b9dbe1d86fc20")
        (revision "1"))
    (package
      (name "r-umi4cpackage")
      (version (git-version "0.0.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/tanaylab/umi4cpackage")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0bjzamdw2lcfhlbzc0vdva87c3wwnij8jsvnrpx4wyyxvpcz13m5"))))
      (properties `((upstream-name . "umi4cPackage")))
      (build-system r-build-system)
      (arguments
       `(#:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'fix-references
             (lambda _
               (substitute* "inst/conf/paths.conf"
                 (("TG3C\\.bowtie2_bin=.*")
                  (string-append "TG3C.bowtie2_bin="
                                 (which "bowtie2") "\n")))
               (substitute* "inst/perl/map3c/TG3C/import3C.pl"
                 (("\"perl")
                  (string-append "\"" (which "perl")))))))))
      (inputs
       (list perl bowtie))
      (propagated-inputs
       (list r-misha r-zoo))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/tanaylab/umi4cpackage")
      (synopsis "Processing and analysis of UMI-4C contact profiles")
      (description "This is a package that lets you process UMI-4C data from
scratch to produce nice plots.")
      (license license:expat))))

(define-public r-shinycell
  (let ((commit
         "aecbd56e66802f28e397f5ae1f19403aadd12163")
        (revision "1"))
    (package
      (name "r-shinycell")
      (version (git-version "2.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/SGDDNB/ShinyCell")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "13jn2ikmvljnzayk485g1mmq5abcp9m1b8n1djdb1agmn83zaki5"))))
      (properties `((upstream-name . "ShinyCell")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-data-table
             r-ggplot2
             r-glue
             r-gridextra
             r-hdf5r
             r-matrix
             r-r-utils
             r-rcolorbrewer
             r-readr
             r-reticulate))
      (home-page "https://github.com/SGDDNB/ShinyCell")
      (synopsis "Shiny interactive web apps for single-cell data")
      (description
       "This package provides Shiny apps for interactive exploration of
single-cell data.")
      (license license:gpl3))))

(define-public r-archr
  (let ((commit "c61b0645d1482f80dcc24e25fbd915128c1b2500")
        (revision "1"))
    (package
      (name "r-archr")
      (version (git-version "1.0.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/GreenleafLab/ArchR")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0sgdfd8iwgj8cssj2zr3gmshg8nv54q6dd8asjf99i39qkni7p9i"))))
      (properties `((upstream-name . "ArchR")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocgenerics
             r-biostrings
             r-chromvar
             r-complexheatmap
             r-data-table
             r-genomicranges
             r-ggplot2
             r-ggrepel
             r-gridextra
             r-gtable
             r-gtools
             r-magrittr
             r-matrix
             r-matrixstats
             r-motifmatchr
             r-nabor
             r-plyr
             r-rcpp
             r-rhdf5
             r-rsamtools
             r-s4vectors
             r-stringr
             r-summarizedexperiment
             r-uwot))
      (home-page "https://github.com/GreenleafLab/ArchR")
      (synopsis "Analyze single-cell regulatory chromatin in R")
      (description
       "This package is designed to streamline scATAC analyses in R.")
      (license license:gpl2+))))

(define-public r-azimuth
  (let ((commit "243ee5db80fcbffa3452c944254a325a3da2ef9e")
        (revision "1"))
    (package
      (name "r-azimuth")
      (version (git-version "0.5.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/satijalab/azimuth")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0vs4813kf2cv2j1z800ihwk62bw4dgmwgkd47rln58581chv39zm"))))
      (properties `((upstream-name . "Azimuth")))
      (build-system r-build-system)
      (propagated-inputs (list r-bsgenome-hsapiens-ucsc-hg38
                               r-dt
                               r-ensdb-hsapiens-v86
                               r-future
                               r-ggplot2
                               r-glmgampoi
                               r-googlesheets4
                               r-hdf5r
                               r-htmltools
                               r-httr
                               r-jaspar2020
                               r-jsonlite
                               r-matrix
                               r-patchwork
                               r-plotly
                               r-presto
                               r-rcpp
                               r-rlang
                               r-scales
                               r-seurat
                               r-seuratdata
                               r-seuratdisk
                               r-seuratobject
                               r-shiny
                               r-shinybs
                               r-shinydashboard
                               r-shinyjs
                               r-signac
                               r-stringr
                               r-tfbstools
                               r-withr))
      (home-page "https://github.com/satijalab/azimuth")
      (synopsis
       "Shiny app showcasing a single-cell data query-reference mapping algorithm")
      (description "Azimuth utilizes an annotated reference dataset.  It
automates the processing, analysis, and interpretation.  This applies
specifically to new single-cell RNA-seq or ATAC-seq experiments.  Azimuth
leverages a reference-based mapping pipeline that inputs acounts matrix and
performs normalization, visualization, cell annotation, and differential
expression.")
      (license license:gpl3))))

(define-public r-icellnet
  ;; This is an arbitrary commit because there is no tag for 2.2.1.
  (let ((commit "e10ee4ae5feaf8130764dcb0736957d2a90b828c")
        (revision "1"))
    (package
      (name "r-icellnet")
      (version (git-version "2.2.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/soumelis-lab/ICELLNET")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0bszxw9zcsd1gxhg9q89jfzi95266wfjn74hp7z8yb99cr3j53k4"))))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'enter-dir
             (lambda _ (chdir "icellnet"))))))
      (propagated-inputs
       (list r-annotationdbi
             r-complexheatmap
             r-circlize
             r-data-table
             r-dplyr
             r-ggplot2
             r-hgu133plus2-db
             r-jetset
             r-psych
             r-reshape2
             r-rlist))
      (home-page "https://github.com/soumelis-lab/ICELLNET")
      (synopsis "Transcriptomic-based framework to dissect cell communication")
      (description "This package provides a a transcriptomic-based framework
to dissect cell communication in a global manner.  It integrates an original
expert-curated database of ligand-receptor interactions taking into account
multiple subunits expression.  Based on transcriptomic profiles (gene
expression), this package computes communication scores between cells
and provides several visualization modes that can be helpful to dig into
cell-cell interaction mechanism and extend biological knowledge.")
      (license license:gpl3))))

(define-public r-scde
  (package
    (name "r-scde")
    (version "1.99.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/hms-dbmi/scde")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-rcpp
           r-rcpparmadillo
           r-mgcv
           r-rook
           r-rjson
           r-cairo
           r-rcolorbrewer
           r-edger
           r-quantreg
           r-nnet
           r-rmtstat
           r-extremes
           r-pcamethods
           r-biocparallel
           r-flexmix))
    (home-page "https://hms-dbmi.github.io/scde/")
    (synopsis "R package for analyzing single-cell RNA-seq data")
    (description "The SCDE package implements a set of statistical methods for
analyzing single-cell RNA-seq data.  SCDE fits individual error models for
single-cell RNA-seq measurements.  These models can then be used for
assessment of differential expression between groups of cells, as well as
other types of analysis.  The SCDE package also contains the pagoda framework
which applies pathway and gene set overdispersion analysis to identify aspects
of transcriptional heterogeneity among single cells.")
    ;; See https://github.com/hms-dbmi/scde/issues/38
    (license license:gpl2)))

(define-public r-miamiplot
  (let ((commit "beede9c5d6431b4d822aa42e064e01baeb5dd4a0")
        (revision "1"))
    (package
      (name "r-miamiplot")
      (version (git-version "1.1.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/juliedwhite/miamiplot")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0wxxk1lk9jbf0imf59qp302ffasvs84idinkvzirs3dw9w3589n9"))))
      (properties `((upstream-name . "miamiplot")))
      (build-system r-build-system)
      (propagated-inputs (list r-checkmate
                               r-dplyr
                               r-ggplot2
                               r-ggrepel
                               r-gridextra
                               r-magrittr
                               r-rlang))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/juliedwhite/miamiplot")
      (synopsis "Create a ggplot2 miami plot")
      (description
       "This package generates a Miami plot with centered chromosome labels.
The output is a ggplot2 object.  Users can specify which data they want
plotted on top vs. bottom, whether to display significance line(s), what
colors to give chromosomes, and what points to label.")
      (license license:gpl2))))

(define-public r-millefy
  (package
    (name "r-millefy")
    (version "0.1.9-beta")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/yuifu/millefy")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0z2y0x99f761pxvg6n37cmnyrnj699jhjk43pvk05sa86iykgizl"))))
    (properties `((upstream-name . "millefy")))
    (build-system r-build-system)
    (propagated-inputs
     (list r-data-table
           r-destiny
           r-dplyr
           r-genomicranges
           r-iranges
           r-magrittr
           r-rsamtools
           r-rtracklayer
           r-tidyr))
    (home-page "https://github.com/yuifu/millefy")
    (synopsis "Make millefy plot with single-cell RNA-seq data")
    (description "@code{Millefy} is a tool for visualizing read coverage of
@dfn{scRNA-seq}(single-cell RNA sequencing) datasets in genomic contexts.  By
dynamically and automatically reorder single cells based on locus-specific
pseudo time, @code{Millefy} highlights cell-to-cell heterogeneity in read coverage
of scRNA-seq data.")
    (license license:expat)))

(define-public r-misha
  (package
    (name "r-misha")
    (version "4.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/tanaylab/misha")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p"))
       ;; Delete bundled executable.
       (snippet
        '(delete-file "exec/bigWigToWig"))))
    (build-system r-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'do-not-use-bundled-bigWigToWig
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "R/misha.R"
               (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig")
                (string-append "\""
                               (assoc-ref inputs "kentutils")
                               "/bin/bigWigToWig"))))))))
    (inputs
     (list kentutils))
    (home-page "https://github.com/tanaylab/misha")
    (synopsis "Toolkit for analysis of genomic data")
    (description "This package is intended to help users to efficiently
analyze genomic data resulting from various experiments.")
    (license license:gpl2)))

(define-public r-scseqcomm
  (let ((commit "01076e703999f1a5aa76419d821b50aebe2b777a")
        (revision "0"))
    (package
      (name "r-scseqcomm")
      (version (git-version "0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://gitlab.com/sysbiobig/scseqcomm")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "1fw5si47d6agnz5fibmp2b1sv08pbpwv1j71w57xbav9044i032q"))
         ;; Delete bundled dependency.
         (modules '((guix build utils)))
         (snippet
          '(delete-file-recursively "other_deps"))))
      (build-system r-build-system)
      (inputs
       (list r-add2ggplot
             r-chorddiag
             r-doparallel
             r-dplyr
             r-foreach
             ;;r-grid ;; listed in DESCRIPTION
             r-gridextra
             r-ggplot2
             r-gtable
             r-htmlwidgets
             r-igraph
             r-matrix
             ;;r-methods ;; listed in DESCRIPTION
             r-org-hs-eg-db
             r-psych
             r-rcolorbrewer
             r-rlang
             r-scico
             r-tidygraph
             r-topgo))
      (native-inputs
       (list r-knitr))
      (home-page "https://gitlab.com/sysbiobig/scseqcomm")
      (synopsis "Inter- and intra- cellular signaling from single cell RNA-seq")
      (description "This package is tools for analysing intercellular and
intracellular signaling from single cell RNA-seq (scRNA-seq) data.")
      (license license:gpl3))))

(define-public r-shaman
  (let ((commit "d6944e8ac7bd1dbd5c6cec646eafc1d19d0ca96f")
        (release "2.0")
        (revision "2"))
    (package
      (name "r-shaman")
      (version (git-version release revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/tanaylab/shaman")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "03sx138dzpfiq23j49z0m0s4j79855mrg64hpj9c83408wzphxi6"))
                (snippet
                 ;; This file will be generated.
                 '(delete-file "inst/doc/shaman-package.R"))))
      (build-system r-build-system)
      (propagated-inputs
       (list r-data-table
             r-domc
             r-ggplot2
             r-gviz
             r-misha
             r-plyr
             r-rann
             r-rcpp
             r-reshape2
             ;; For vignettes
             r-rmarkdown
             r-knitr))
      (home-page "https://github.com/tanaylab/shaman")
      (synopsis "Sampling HiC contact matrices for a-parametric normalization")
      (description "The Shaman package implements functions for
resampling Hi-C matrices in order to generate expected contact
distributions given constraints on marginal coverage and
contact-distance probability distributions.  The package also provides
support for visualizing normalized matrices and statistical analysis
of contact distributions around selected landmarks.")
      ;; Any version of the GPL
      (license license:gpl3+))))

(define-public r-centipede
  (package
    (name "r-centipede")
    (version "1.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://download.r-forge.r-project.org/"
                                  "src/contrib/CENTIPEDE_" version ".tar.gz"))
              (sha256
               (base32
                "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
    (build-system r-build-system)
    (home-page "https://centipede.uchicago.edu/")
    (synopsis "Predict transcription factor binding sites")
    (description
     "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
of the genome that are bound by particular transcription factors.  It starts
by identifying a set of candidate binding sites, and then aims to classify the
sites according to whether each site is bound or not bound by a transcription
factor.  CENTIPEDE is an unsupervised learning algorithm that discriminates
between two different types of motif instances using as much relevant
information as possible.")
    (license (list license:gpl2+ license:gpl3+))))

(define-public r-demultiplex
  (let ((commit "6e2a1422c8e6f418cfb271997eebc91f9195f299")
        (revision "1"))
    (package
      (name "r-demultiplex")
      (version (git-version "1.0.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/chris-mcginnis-ucsf/MULTI-seq")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "01kv88wp8vdaq07sjk0d3d1cb553mq1xqg0war81pgmg63bgi38w"))))
      (properties `((upstream-name . "deMULTIplex")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-kernsmooth r-reshape2 r-rtsne r-shortread r-stringdist))
      (home-page "https://github.com/chris-mcginnis-ucsf/MULTI-seq")
      (synopsis "MULTI-seq pre-processing and classification tools")
      (description
       "deMULTIplex is an R package for analyzing single-cell RNA sequencing
data generated with the MULTI-seq sample multiplexing method.  The package
includes software to

@enumerate
@item Convert raw MULTI-seq sample barcode library FASTQs into a sample
  barcode UMI count matrix, and
@item Classify cell barcodes into sample barcode groups.
@end enumerate
")
      (license license:cc0))))

(define-public r-demultiplex2
  (let ((commit "c1ce09e8b5784b485680cf96b90bbc12eed96907")
        (revision "2"))
    (package
      (name "r-demultiplex2")
      (version (git-version "1.0.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/Gartner-Lab/deMULTIplex2")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0fid5yh0hqg477h5xxq6c8yh8zs5jawjskzns05rndxhbzm51lpr"))))
      (properties `((upstream-name . "deMULTIplex2")))
      (build-system r-build-system)
      (propagated-inputs (list r-data-table
                               r-devtools
                               r-dplyr
                               r-ggextra
                               r-ggplot2
                               r-gridextra
                               r-magrittr
                               r-mass
                               r-matrix
                               r-rcolorbrewer
                               r-shortread
                               r-stringdist
                               r-tidyr
                               r-uwot
                               r-viridis
                               r-xvector))
      (home-page "https://github.com/Gartner-Lab/deMULTIplex2")
      (synopsis "Robust sample demultiplexing for scRNA-seq")
      (description
       "This package implements a bioinformatics algorithm for demultiplexing
multiplexed single cell datasets.  It is built on a statistical model of tag
read counts derived from the physical mechanism of tag cross-contamination.")
      (license license:cc0))))

(define-public r-demuxmix
  (let ((commit "09a7918ca6e0cd23e6bbaed2b97388bc499e248e")
        (revision "1"))
    (package
      (name "r-demuxmix")
      (version (git-version "1.1.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/huklein/demuxmix")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "03kfnns7m2447jsc3xplyv9qx8hvvdjmii7j837g3bb6smyxss96"))))
      (properties `((upstream-name . "demuxmix")))
      (build-system r-build-system)
      (propagated-inputs (list r-ggplot2 r-gridextra r-mass r-matrix))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/huklein/demuxmix")
      (synopsis
       "Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models")
      (description
       "This package is used for demultiplexing single-cell sequencing
experiments of pooled cells.  These cells are labeled with barcode
oligonucleotides.  The package implements methods to fit regression mixture
models for a probabilistic classification of cells, including multiplet
detection.  Demultiplexing error rates can be estimated, and methods for
quality control are provided.")
      (license license:artistic2.0))))

(define-public gdc-client
  (package
    (name "gdc-client")
    (version "1.6.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/NCI-GDC/gdc-client.git")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0cagawlzjwj3wam10lv64xgbfx4zcnzxi5sjpsdhq7rn4z24mzc2"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "requirements.txt"
               (("==") ">=")))))))
    (inputs
     (list python-cryptography
           python-intervaltree
           python-jsonschema
           python-lxml
           python-ndg-httpsclient
           python-progressbar2
           python-pyasn1
           python-pyopenssl
           python-pyyaml
           python-requests
           python-termcolor))
    (home-page "https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool")
    (synopsis "GDC data transfer tool")
    (description "The gdc-client provides several convenience functions over
the GDC API which provides general download/upload via HTTPS.")
    (license license:asl2.0)))

(define-public vsearch
  (package
    (name "vsearch")
    (version "2.9.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/torognes/vsearch")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
       (patches (search-patches "vsearch-unbundle-cityhash.patch"))
       (snippet
        '(begin
           ;; Remove bundled cityhash sources.  The vsearch source is adjusted
           ;; for this in the patch.
           (delete-file "src/city.h")
           (delete-file "src/citycrc.h")
           (delete-file "src/city.cc")
           #t))))
    (build-system gnu-build-system)
    (inputs
     (list zlib bzip2 cityhash))
    (native-inputs
     (list autoconf automake))
    (synopsis "Sequence search tools for metagenomics")
    (description
     "VSEARCH supports DNA sequence searching, clustering, chimera detection,
dereplication, pairwise alignment, shuffling, subsampling, sorting and
masking.  The tool takes advantage of parallelism in the form of SIMD
vectorization as well as multiple threads to perform accurate alignments at
high speed.  VSEARCH uses an optimal global aligner (full dynamic programming
Needleman-Wunsch).")
    (home-page "https://github.com/torognes/vsearch")
    ;; vsearch uses non-portable SSE intrinsics so building fails on other
    ;; platforms.
    (supported-systems '("x86_64-linux"))
    ;; Dual licensed; also includes public domain source.
    (license (list license:gpl3 license:bsd-2))))

(define-public pairadise
  (package
    (name "pairadise")
    (version "1.0.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/Xinglab/PAIRADISE")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0ycwcqabm4zdng0a7j593g35d5yzvvwm7dyi3b8s19zdi4rjzrwd"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _ (chdir "pairadise")))
         (add-before 'build '2to3
           (lambda _ (invoke "2to3" "--write" "--nobackups" "."))))))
    (inputs (list star))
    (propagated-inputs (list python-pysam))
    (home-page "https://github.com/Xinglab/PAIRADISE")
    (synopsis "Paired replicate analysis of allelic differential splicing events")
    (description
     "PAIRADISE is a method for detecting @dfn{allele-specific alternative
splicing} (ASAS) from RNA-seq data.  Unlike conventional approaches that
detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals
across multiple individuals in a population.  By treating the two alleles of
an individual as paired, and multiple individuals sharing a heterozygous SNP
as replicates, PAIRADISE formulates ASAS detection as a statistical problem
for identifying differential alternative splicing from RNA-seq data with
paired replicates.")
    (license license:gpl3+)))

(define-public r-pairadise
  (package
    (inherit pairadise)
    (name "r-pairadise")
    (build-system r-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _ (chdir "pairadise/src/pairadise_model"))))))
    (inputs '())
    (propagated-inputs (list r-doparallel r-foreach r-iterators r-nloptr))
    (license license:expat)))

(define-public r-pairwiseadonis
  ;; There is no tag for version 0.4.1, nor is there a release archive.
  (let ((commit "cb190f7668a0c82c0b0853927db239e7b9ec3e83")
        (revision "1"))
    (package
      (name "r-pairwiseadonis")
      ;; The versioning scheme of this package is inconsistent, with versions
      ;; progressing from 0.21 to 0.3 and then to 0.4.1, which does not follow
      ;; a standard numerical order or convention (e.g., semantic versioning).
      (version (git-version "0.4.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/pmartinezarbizu/pairwiseAdonis")
               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32 "11hl6qqmr5vns476921802y0qmb46i1jf0rf7xfkyswlh6xkcl99"))))
      (properties `((upstream-name . "pairwiseAdonis")))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        ;; Move into the subdirectory containing the R package files
        '(modify-phases %standard-phases
           (add-after 'unpack 'move-to-subdir
             (lambda _ (chdir "pairwiseAdonis"))))))
      (propagated-inputs
       (list r-cluster
             r-permute
             r-vegan))
      (synopsis "Pairwise multilevel comparison using adonis")
      (description
       "This package implements two functions:
@itemize
@item @code{pairwise.adonis} is a wrapper function for multilevel pairwise
comparison using adonis2 from package vegan.  The function returns adjusted
p-values using @code{p.adjust()}.  It does not accept interaction between factors
neither strata.
@item @code{pairwise.adonis2} accepts a model formula like in adonis from vegan.
You can use interactions between factors and define strata to constrain
permutations.  For pairwise comparison a list of unique pairwise combination of
factors is produced.
@end itemize")
      (home-page "https://github.com/pmartinezarbizu/pairwiseAdonis")
      (license license:gpl2+))))

(define-public pardre
  (package
    (name "pardre")
    (version "2.2.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
                           version ".tar.gz"))
       (sha256
        (base32
         "105s4f8zs8hh0sc32r9p725n7idza9cj5jvp5z1m5pljjhgk3if5"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; tests require "prove"
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (install-file "ParDRe" bin)))))))
    (inputs
     (list openmpi-c++ zlib))
    (synopsis "Parallel tool to remove duplicate DNA reads")
    (description
     "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
Duplicate reads can be seen as identical or nearly identical sequences with
some mismatches.  This tool lets users avoid the analysis of unnecessary
reads, reducing the time of subsequent procedures with the
dataset (e.g. assemblies, mappings, etc.).  The tool is implemented with MPI
in order to exploit the parallel capabilities of multicore clusters.  It is
faster than multithreaded counterparts (end of 2015) for the same number of
cores and, thanks to the message-passing technology, it can be executed on
clusters.")
    (home-page "https://sourceforge.net/projects/pardre/")
    (license license:gpl3+)))

(define-public ngshmmalign
  (package
    (name "ngshmmalign")
    (version "0.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/cbg-ethz/ngshmmalign/"
                           "releases/download/" version
                           "/ngshmmalign-" version ".tar.bz2"))
       (sha256
        (base32
         "0jryvlssi2r2ii1dxnx39yk6bh4yqgq010fnxrgfgbaj3ykijlzv"))))
    (build-system cmake-build-system)
    (arguments '(#:tests? #false))      ; there are none
    (inputs
     (list boost))
    (home-page "https://github.com/cbg-ethz/ngshmmalign/")
    (synopsis "Profile HMM aligner for NGS reads")
    (description
     "ngshmmalign is a profile HMM aligner for NGS reads designed particularly
for small genomes (such as those of RNA viruses like HIV-1 and HCV) that
experience substantial biological insertions and deletions.")
    (license license:gpl2+)))

(define-public prinseq
  (package
    (name "prinseq")
    (version "0.20.4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/prinseq/standalone/"
                           "prinseq-lite-" version ".tar.gz"))
       (sha256
        (base32
         "0vxmzvmm67whxrqdaaamwgjk7cf0fzfs5s673jgg00kz7g70splv"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #false                  ; no check target
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build)
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (scripts (find-files "." "prinseq.*.pl"))
                    (guile (search-input-file inputs "bin/guile")))
               (substitute* scripts
                 (("\"perl -pe")
                  (string-append "\"" (which "perl") " -pe")))
               (for-each (lambda (file)
                           (chmod file #o555)
                           (install-file file bin)
                           (wrap-script (string-append bin "/" (basename file))
                                        #:guile guile
                                        `("PERL5LIB" ":" prefix
                                          (,(getenv "PERL5LIB")))))
                         scripts)))))))
    (inputs
     (list guile-3.0 ; for wrapper scripts
           perl
           perl-cairo
           perl-data-dumper
           perl-digest-md5
           perl-getopt-long
           perl-json
           perl-statistics-pca))
    (home-page "https://prinseq.sourceforge.net/")
    (synopsis "Preprocess sequence data in FASTA or FASTQ formats")
    (description
     "PRINSEQ is a bioinformatics tool to help you preprocess your genomic or
metagenomic sequence data in FASTA or FASTQ formats.  The tool is written in
Perl and can be helpful if you want to filter, reformat, or trim your sequence
data.  It also generates basic statistics for your sequences.")
    (license license:gpl3+)))

(define-public shorah
  (package
    (name "shorah")
    (version "1.99.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/cbg-ethz/shorah"
                           "/releases/download/v" version
                           "/shorah-" version ".tar.xz"))
       (sha256
        (base32
         "158dir9qcqspknlnyfr9zwk41x48nrh5wcg10k2grh9cidp9daiq"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-test-wrapper
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (substitute* "examples/run_end2end_test"
                 (("\\$\\{interpreter\\} ../\\$\\{testscript\\}")
                  (string-append bin "/${testscript}"))))))
         (delete 'check)
         (add-after 'install 'wrap-programs
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (site (string-append
                           out "/lib/python"
                           ,(version-major+minor
                             (package-version python))
                           "/site-packages"))
                    (pythonpath (getenv "GUIX_PYTHONPATH"))
                    (script (string-append out "/bin/shorah")))
               (chmod script #o555)
               (wrap-program script `("GUIX_PYTHONPATH" ":" prefix (,site ,pythonpath))))))
         (add-after 'wrap-programs 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "make" "check")))))))
    (inputs
     (list bash-minimal
           boost
           htslib
           python
           python-biopython
           python-numpy
           zlib))
    (native-inputs
     (list pkg-config))
    (home-page "")
    (synopsis "Short reads assembly into haplotypes")
    (description
     "ShoRAH is a project for the analysis of next generation sequencing data.
It is designed to analyse genetically heterogeneous samples.  Its tools
provide error correction, haplotype reconstruction and estimation of the
frequency of the different genetic variants present in a mixed sample.")
    (license license:gpl3+)))

(define-public ruby-bio-kseq
  (package
    (name "ruby-bio-kseq")
    (version "0.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (rubygems-uri "bio-kseq" version))
       (sha256
        (base32
         "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
    (build-system ruby-build-system)
    (arguments
     `(#:test-target "spec"))
    (native-inputs
     (list bundler ruby-rspec ruby-rake-compiler))
    (inputs
     (list zlib))
    (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
    (description
     "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
FASTQ parsing code.  It provides a fast iterator over sequences and their
quality scores.")
    (home-page "https://github.com/gusevfe/bio-kseq")
    (license license:expat)))

(define-public bio-locus
  (package
    (name "bio-locus")
    (version "0.0.7")
    (source
     (origin
       (method url-fetch)
       (uri (rubygems-uri "bio-locus" version))
       (sha256
        (base32
         "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
    (build-system ruby-build-system)
    (native-inputs
     (list ruby-rspec))
    (synopsis "Tool for fast querying of genome locations")
    (description
     "Bio-locus is a tabix-like tool for fast querying of genome
locations.  Many file formats in bioinformatics contain records that
start with a chromosome name and a position for a SNP, or a start-end
position for indels.  Bio-locus allows users to store this chr+pos or
chr+pos+alt information in a database.")
    (home-page "https://github.com/pjotrp/bio-locus")
    (license license:expat)))

(define-public bio-blastxmlparser
  (package
    (name "bio-blastxmlparser")
    (version "2.0.4")
    (source (origin
              (method url-fetch)
              (uri (rubygems-uri "bio-blastxmlparser" version))
              (sha256
               (base32
                "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
    (build-system ruby-build-system)
    (propagated-inputs
     (list ruby-bio-logger ruby-nokogiri))
    (inputs
     (list ruby-rspec))
    (synopsis "Fast big data BLAST XML parser and library")
    (description
     "Very fast parallel big-data BLAST XML file parser which can be used as
command line utility.  Use blastxmlparser to: Parse BLAST XML; filter output;
generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
    (home-page "https://github.com/pjotrp/blastxmlparser")
    (license license:expat)))

(define-public bioruby
  (package
    (name "bioruby")
    (version "2.0.4")
    (source
     (origin
       (method url-fetch)
       (uri (rubygems-uri "bio" version))
       (sha256
        (base32
         "08aknxk2ingwscwfqpw5vnax6jpk1sxfaialravladb63hcl8dx9"))))
    (build-system ruby-build-system)
    (propagated-inputs
     (list ruby-libxml))
    (native-inputs
     (list which))  ; required for test phase
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'build 'patch-test-command
            (lambda _
              (substitute* '("test/functional/bio/test_command.rb")
                (("/bin/sh") (which "sh")))
              (substitute* '("test/functional/bio/test_command.rb")
                (("/bin/ls") (which "ls")))
              (substitute* '("test/functional/bio/test_command.rb")
                (("which") (which "which")))
              (substitute* '("test/functional/bio/test_command.rb"
                             "test/data/command/echoarg2.sh")
                (("/bin/echo") (which "echo"))))))))
    (synopsis "Ruby library, shell and utilities for bioinformatics")
    (description "BioRuby comes with a comprehensive set of Ruby development
tools and libraries for bioinformatics and molecular biology.  BioRuby has
components for sequence analysis, pathway analysis, protein modelling and
phylogenetic analysis; it supports many widely used data formats and provides
easy access to databases, external programs and public web services, including
BLAST, KEGG, GenBank, MEDLINE and GO.")
    (home-page "http://bioruby.org/")
    ;; Code is released under Ruby license, except for setup
    ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
    (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))

(define-public centrifuge
  (package
    (name "centrifuge")
    (version "1.0.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/DaehwanKimLab/centrifuge.git")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "167610gbz1rrh6ir3j7jcmhzg3x5msn7x7a3dpv7wmwdndnnqvg0"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #false                   ; no check target
      #:make-flags
      #~(list (string-append "prefix=" #$output))
      #:phases
      '(modify-phases %standard-phases
         (delete 'configure))))
    (inputs (list python-wrapper))
    (native-inputs
     (list pandoc perl                  ;for documentation
           which))
    (home-page "https://github.com/DaehwanKimLab/centrifuge/")
    (synopsis "Classifier for metagenomic sequences")
    (description "Centrifuge is a microbial classification engine that enables
rapid, accurate and sensitive labeling of reads and quantification of species
on desktop computers.  The system uses an indexing scheme based on the
@dfn{Burrows-Wheeler transform} (BWT) and the @dfn{Ferragina-Manzini} (FM)
index, optimized specifically for the metagenomic classification problem.
Centrifuge requires a relatively small index (4.7 GB for all complete
bacterial and viral genomes plus the human genome) and classifies sequences at
very high speed, allowing it to process the millions of reads from a typical
high-throughput DNA sequencing run within a few minutes.")
    (license license:gpl3+)))

(define-public bio-vcf
  (package
    (name "bio-vcf")
    (version "0.9.5")
    (source
      (origin
        (method url-fetch)
        (uri (rubygems-uri "bio-vcf" version))
        (sha256
         (base32
          "1glw5pn9s8z13spxk6yyfqaz80n9lga67f33w35nkpq9dwi2vg6g"))))
    (build-system ruby-build-system)
    (native-inputs
     (list ruby-cucumber))
    (synopsis "Smart VCF parser DSL")
    (description
     "Bio-vcf provides a @acronym{DSL, domain specific language} for processing
the VCF format.  Record named fields can be queried with regular expressions.
Bio-vcf is a new generation VCF parser, filter and converter.  Bio-vcf is not
only very fast for genome-wide (WGS) data, it also comes with a filtering,
evaluation and rewrite language and can output any type of textual data,
including VCF header and contents in RDF and JSON.")
    (home-page "https://github.com/vcflib/bio-vcf")
    (license license:expat)))

(define-public r-phantompeakqualtools
  (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42")
        (revision "1"))
    (package
      (name "r-phantompeakqualtools")
      (version (git-version "1.2.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/kundajelab/phantompeakqualtools")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; There are no tests.
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (delete 'build)
           (replace 'install
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let ((script (string-append (assoc-ref outputs "out")
                                            "/share/scripts")))
                 (install-file "run_spp.R" script)))))))
      (inputs
       `(("r" ,r-minimal)))
      (propagated-inputs
       (list r-catools
             r-snow
             r-snowfall
             r-bitops
             r-rsamtools
             r-spp
             gawk
             samtools
             boost
             gzip))
      (home-page "https://github.com/kundajelab/phantompeakqualtools")
      (synopsis "Informative enrichment for ChIP-seq data")
      (description "This package computes informative enrichment and quality
measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.  It can also be
used to obtain robust estimates of the predominant fragment length or
characteristic tag shift values in these assays.")
      (license license:bsd-3))))

(define-public r-r4rna
  (package
    (name "r-r4rna")
    (version "0.1.4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
                           version ".tar.gz"))
       (sha256
        (base32
         "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-optparse r-rcolorbrewer))
    (home-page "https://www.e-rna.org/r-chie/index.cgi")
    (synopsis "Analysis framework for RNA secondary structure")
    (description
     "The R4RNA package aims to be a general framework for the analysis of RNA
secondary structure and comparative analysis in R.")
    (license license:gpl3+)))

(define-public rcas-web
  (let ((commit "71c93e3835653beb4eaa6e89b860bee3779729b8")
        (revision "2"))
    (package
      (name "rcas-web")
      (version (git-version "0.1.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/BIMSBbioinfo/rcas-web")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0232g0f7g0w5cgaib462zbfssvfq8i0iqv5b5wfmbrbn0sw99l9a"))))
      (build-system gnu-build-system)
      (arguments
       (list
        #:phases
        #~(modify-phases %standard-phases
            (add-after 'install 'wrap-executable
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((json   #$(this-package-input "guile-json"))
                       (redis  #$(this-package-input "guile-redis"))
                       (path   (string-append
                                json  "/share/guile/site/3.0:"
                                redis "/share/guile/site/3.0")))
                  (wrap-program (string-append #$output "/bin/rcas-web")
                    `("GUILE_LOAD_PATH" ":" = (,path))
                    `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
                    `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))))))))
      (inputs
       (list bash-minimal
             r-minimal
             r-rcas
             guile-3.0
             guile-json-4
             guile-redis))
      (native-inputs
       (list autoconf
             automake
             pkg-config))
      (home-page "https://github.com/BIMSBbioinfo/rcas-web")
      (synopsis "Web interface for RNA-centric annotation system (RCAS)")
      (description "This package provides a simple web interface for the
@dfn{RNA-centric annotation system} (RCAS).")
      (license license:agpl3+))))

(define-public r-chipkernels
  (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
        (revision "1"))
    (package
      (name "r-chipkernels")
      (version (git-version "1.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/ManuSetty/ChIPKernels")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
      (build-system r-build-system)
      (propagated-inputs
       (list r-iranges
             r-xvector
             r-biostrings
             r-bsgenome
             r-gtools
             r-genomicranges
             r-sfsmisc
             r-kernlab
             r-s4vectors
             r-biocgenerics))
      (home-page "https://github.com/ManuSetty/ChIPKernels")
      (synopsis "Build string kernels for DNA Sequence analysis")
      (description "ChIPKernels is an R package for building different string
kernels used for DNA Sequence analysis.  A dictionary of the desired kernel
must be built and this dictionary can be used for determining kernels for DNA
Sequences.")
      (license license:gpl2+))))

(define-public r-seqgl
  (package
    (name "r-seqgl")
    (version "1.1.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/ManuSetty/SeqGL")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biostrings
           r-chipkernels
           r-genomicranges
           r-spams
           r-wgcna
           r-fastcluster))
    (home-page "https://github.com/ManuSetty/SeqGL")
    (synopsis "Group lasso for Dnase/ChIP-seq data")
    (description "SeqGL is a group lasso based algorithm to extract
transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
This package presents a method which uses group lasso to discriminate between
bound and non bound genomic regions to accurately identify transcription
factors bound at the specific regions.")
    (license license:gpl2+)))

(define-public r-seraster
  ;; There are no tags or releases.
  (let ((commit "4fdc1ffe5d3feb65de9880329d221cf276b393a1")
        (revision "1"))
    (package
      (name "r-seraster")
      (version (git-version "0.99.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/JEFworks-Lab/SEraster")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0y33lk8q0h9nfzmf7slxxvw3l0djassp4l63nsjpm3p6z4pah5s4"))))
      (properties `((upstream-name . "SEraster")))
      (build-system r-build-system)
      (propagated-inputs (list r-biocparallel
                               r-ggplot2
                               r-matrix
                               r-rearrr
                               r-sf
                               r-spatialexperiment
                               r-summarizedexperiment))
      (home-page "https://github.com/JEFworks-Lab/SEraster")
      (synopsis
       "Rasterization framework for scalable spatial omics data analysis")
      (description
       "This package is a rasterization preprocessing framework that aggregates
cellular information into spatial pixels to reduce resource requirements for
spatial omics data analysis.  SEraster reduces the number of points in spatial
omics datasets for downstream analysis through a process of rasterization where
single cells gene expression or cell-type labels are aggregated into equally
sized pixels based on a user-defined resolution.  SEraster can be incorporated
with other packages to conduct downstream analyses for spatial omics datasets,
such as detecting spatially variable genes.")
      (license license:gpl3))))

(define-public emboss
  (package
    (name "emboss")
    (version "6.5.7")
    (source (origin
              (method url-fetch)
              (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
                                  (version-major+minor version) ".0/"
                                  "EMBOSS-" version ".tar.gz"))
              (sha256
               (base32
                "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       ,#~(list (string-append "--with-hpdf="
                               #$(this-package-input "libharu")))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-checks
           (lambda _
             ;; The PNGDRIVER tests check for the presence of libgd, libpng
             ;; and zlib, but assume that they are all found at the same
             ;; prefix.
             (substitute* "configure.in"
               (("CHECK_PNGDRIVER")
                "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
AM_CONDITIONAL(AMPNG, true)"))
             #t))
         (add-after 'fix-checks 'disable-update-check
           (lambda _
             ;; At build time there is no connection to the Internet, so
             ;; looking for updates will not work.
             (substitute* "Makefile.am"
               (("\\$\\(bindir\\)/embossupdate") ""))
             #t))
         (add-after 'disable-update-check 'autogen
           (lambda _ (invoke "autoreconf" "-vif") #t)))))
    (inputs
     (list perl
           libpng
           gd
           libx11
           libharu
           zlib))
    (native-inputs
     (list autoconf automake libtool pkg-config))
    (home-page "https://emboss.sourceforge.net")
    (synopsis "Molecular biology analysis suite")
    (description "EMBOSS is the \"European Molecular Biology Open Software
Suite\".  EMBOSS is an analysis package specially developed for the needs of
the molecular biology (e.g. EMBnet) user community.  The software
automatically copes with data in a variety of formats and even allows
transparent retrieval of sequence data from the web.  It also provides a
number of libraries for the development of software in the field of molecular
biology.  EMBOSS also integrates a range of currently available packages and
tools for sequence analysis into a seamless whole.")
    (license license:gpl2+)))

(define-public bits
  (let ((revision "1")
        (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
    (package
      (name "bits")
      ;; The version is 2.13.0 even though no release archives have been
      ;; published as yet.
      (version (git-version "2.13.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/arq5x/bits")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ;no tests included
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (add-after 'unpack 'remove-cuda
             (lambda _
               (substitute* "Makefile"
                 ((".*_cuda") "")
                 (("(bits_test_intersections) \\\\" _ match) match))
               #t))
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (copy-recursively
                "bin" (string-append (assoc-ref outputs "out") "/bin"))
               #t)))))
      (inputs
       (list gsl zlib))
      (home-page "https://github.com/arq5x/bits")
      (synopsis "Implementation of binary interval search algorithm")
      (description "This package provides an implementation of the
BITS (Binary Interval Search) algorithm, an approach to interval set
intersection.  It is especially suited for the comparison of diverse genomic
datasets and the exploration of large datasets of genome
intervals (e.g. genes, sequence alignments).")
      (license license:gpl2))))

(define-public piranha
  ;; There is no release tarball for the latest version.  The latest commit is
  ;; older than one year at the time of this writing.
  (let ((revision "1")
        (commit   "0466d364b71117d01e4471b74c514436cc281233"))
    (package
      (name "piranha")
      (version (git-version "1.2.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/smithlabcode/piranha")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
      (build-system gnu-build-system)
      (arguments
       `(#:test-target "test"
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'copy-smithlab-cpp
             (lambda* (#:key inputs #:allow-other-keys)
               (for-each (lambda (file)
                           (install-file file "./src/smithlab_cpp/"))
                         (find-files (assoc-ref inputs "smithlab-cpp")))))
           (add-after 'install 'install-to-store
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
                      (bin (string-append out "/bin")))
                 (for-each (lambda (file)
                             (install-file file bin))
                           (find-files "bin" ".*"))))))
         #:configure-flags
         ,#~(list (string-append "--with-bam_tools_headers="
                                 #$(this-package-input "bamtools") "/include/bamtools")
                  (string-append "--with-bam_tools_library="
                                 #$(this-package-input "bamtools") "/lib/bamtools"))))
      (inputs
       `(("bamtools" ,bamtools)
         ("samtools" ,samtools-0.1)
         ("gsl" ,gsl)
         ("smithlab-cpp"
          ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/smithlabcode/smithlab_cpp")
                     (commit commit)))
               (file-name (string-append "smithlab_cpp-" commit "-checkout"))
               (sha256
                (base32
                 "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
      (native-inputs
       `(("python" ,python-2)))
      (home-page "https://github.com/smithlabcode/piranha")
      (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
      (description
       "Piranha is a peak-caller for genomic data produced by CLIP-seq and
RIP-seq experiments.  It takes input in BED or BAM format and identifies
regions of statistically significant read enrichment.  Additional covariates
may optionally be provided to further inform the peak-calling process.")
      (license license:gpl3+))))

(define-public filevercmp
  (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")
        (revision "1"))
    (package
      (name "filevercmp")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/ekg/filevercmp")
                      (commit commit)))
                (file-name (git-file-name name commit))
                (sha256
                 (base32
                  "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; There are no tests to run.
         #:phases
         (modify-phases %standard-phases
           (delete 'configure) ; There is no configure phase.
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((out (assoc-ref outputs "out")))
                 (install-file "filevercmp" (string-append out "/bin"))
                 (install-file "filevercmp.h" (string-append out "/include"))
                 #t))))))
      (home-page "https://github.com/ekg/filevercmp")
      (synopsis "This program compares version strings")
      (description "This program compares version strings.  It intends to be a
replacement for strverscmp.")
      (license license:gpl3+))))

(define-public multiqc
  (package
    (name "multiqc")
    (version "1.14")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "multiqc" version))
       (sha256
        (base32
         "0qlk2h0765hxp1w9hqf925rh8hq642lzgs6ppg91wln9y02s9fyw"))))
    (build-system pyproject-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key inputs tests? #:allow-other-keys)
             (when tests?
               (setenv "HOME" "/tmp")
               (let ((here (getcwd)))
                 (copy-recursively (assoc-ref inputs "tests") "/tmp/tests")
                 (with-directory-excursion "/tmp/tests"
                   (invoke "multiqc" "data" "--ignore" "data/modules")))))))))
    (inputs
     (list python-click
           python-coloredlogs
           python-future
           python-jinja2
           python-lzstring
           python-markdown
           python-matplotlib
           python-networkx
           python-numpy
           python-pyyaml
           python-requests
           python-rich
           python-rich-click
           python-simplejson
           python-spectra))
    (native-inputs
     `(("python-pytest" ,python-pytest)
       ("tests"
        ,(let ((commit "c3e7400affe3f3ca996973805797af61b93070ba"))
           (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/ewels/MultiQC_TestData")
                   (commit commit)))
             (file-name (git-file-name "multiqc-test-data" commit))
             (sha256
              (base32
               "0wwqbkbfnqj5ax6l0da4csbmv1sw7ya7mwvdwryckaiqmkxy80va")))))))
    (home-page "https://multiqc.info")
    (synopsis "Aggregate bioinformatics analysis reports")
    (description
     "MultiQC is a tool to aggregate bioinformatics results across many
samples into a single report.  It contains modules for a large number of
common bioinformatics tools.")
    (license license:gpl3+)))

(define-public variant-tools
  (package
    (name "variant-tools")
    (version "3.1.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/vatlab/varianttools")
             ;; There is no tag corresponding to version 3.1.2
             (commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
    (build-system python-build-system)
    (inputs
     (list boost
           c-blosc
           gsl
           hdf5
           hdf5-blosc
           python-cython
           zlib))
    (propagated-inputs
     (list python-numpy python-pycurl python-pyzmq python-scipy
           python-tables))
    (home-page "https://vatlab.github.io/vat-docs/")
    (synopsis "Analyze genetic variants from Next-Gen sequencing studies")
    (description
     "Variant tools is a tool for the manipulation, annotation,
selection, simulation, and analysis of variants in the context of next-gen
sequencing analysis.  Unlike some other tools used for next-gen sequencing
analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
    (license license:gpl3+)))

(define-public r-chromvarmotifs
  (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
        (revision "1"))
    (package
      (name "r-chromvarmotifs")
      (version (git-version "0.2.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/GreenleafLab/chromVARmotifs")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q"))))
      (properties `((upstream-name . "chromVARmotifs")))
      (build-system r-build-system)
      (propagated-inputs
       `(("r-tfbstools" ,r-tfbstools)))
      (home-page "https://github.com/GreenleafLab/chromVARmotifs")
      (synopsis "Stores motif collections for use with motifmatchr or chromVAR")
      (description
       "This package stores motif collections as lists of @dfn{position
frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools}
package for use in R with packages like @code{motifmatchr} or
@code{chromVAR}.")
      (license license:expat))))

(define-public r-raremetals2
  (package
    (name "r-raremetals2")
    (version "0.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://genome.sph.umich.edu/w/images/"
                           "b/b7/RareMETALS2_" version ".tar.gz"))
       (sha256
        (base32
         "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
    (properties `((upstream-name . "RareMETALS2")))
    (build-system r-build-system)
    (propagated-inputs
     (list r-seqminer r-mvtnorm r-mass r-compquadform r-getopt))
    (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
    (synopsis "Analyze gene-level association tests for binary trait")
    (description
     "The R package rareMETALS2 is an extension of the R package rareMETALS.
It was designed to meta-analyze gene-level association tests for binary trait.
While rareMETALS offers a near-complete solution for meta-analysis of
gene-level tests for quantitative trait, it does not offer the optimal
solution for binary trait.  The package rareMETALS2 offers improved features
for analyzing gene-level association tests in meta-analyses for binary
trait.")
    (license license:gpl3)))

(define-public r-rnacrosslinkoo
  (let ((commit "a317e0fa6ddf34c309529d57390769e2b2b5bfb7")
        (revision "1"))
    (package
      (name "r-rnacrosslinkoo")
      (version (git-version "0.1.3" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/cran/rnaCrosslinkOO")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0csv9924z0ish960k034qzv3gxh1yabnxni8hsrn5j6xl1r3cdpl"))))
      (properties `((upstream-name . "rnaCrosslinkOO")))
      (build-system r-build-system)
      (propagated-inputs (list r-classdiscovery
                               r-doparallel
                               r-foreach
                               r-genomicranges
                               r-ggplot2
                               r-ggrepel
                               r-heatmap3
                               r-igraph
                               r-iranges
                               r-mass
                               r-mixtools
                               r-patchwork
                               r-r4rna
                               r-rcolorbrewer
                               r-reshape2
                               r-rrna
                               r-s4vectors
                               r-seqinr
                               r-tidyverse
                               r-topdom))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/cran/rnaCrosslinkOO")
      (synopsis "Analysis of RNA crosslinking data")
      (description
       "The package is ideal for analyzing RNA structure and chemical probing data.")
      (license license:gpl3))))

(define-public r-rnaseqdtu
  (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac")
        (revision "1"))
    (package
      (name "r-rnaseqdtu")
      (version (git-version "2.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/mikelove/rnaseqDTU/")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0"))))
      (properties `((upstream-name . "rnaseqDTU")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-deseq2
             r-devtools
             r-dexseq
             r-drimseq
             r-edger
             r-rafalib
             r-stager))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/mikelove/rnaseqDTU/")
      (synopsis "RNA-seq workflow for differential transcript usage")
      (description
       "This package provides an RNA-seq workflow for differential transcript
usage (DTU) following Salmon quantification.  This workflow performs a DTU
analysis on simulated data.  It also shows how to use stageR to perform
two-stage testing of DTU, a statistical framework to screen at the gene level
and then confirm which transcripts within the significant genes show evidence
of DTU.")
      (license license:artistic2.0))))

(define-public r-dropbead
  (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
        (revision "2"))
    (package
      (name "r-dropbead")
      (version (string-append "0-" revision "." (string-take commit 7)))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/rajewsky-lab/dropbead")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
      (build-system r-build-system)
      (propagated-inputs
       (list r-ggplot2 r-rcolorbrewer r-gridextra r-gplots r-plyr))
      (home-page "https://github.com/rajewsky-lab/dropbead")
      (synopsis "Basic exploration and analysis of Drop-seq data")
      (description "This package offers a quick and straight-forward way to
explore and perform basic analysis of single cell sequencing data coming from
droplet sequencing.  It has been particularly tailored for Drop-seq.")
      (license license:gpl3))))

(define-public r-cellchat
  (let ((commit
         "21edd226ca408e4c413408f98562d71ee0b54e5d")
        (revision "1"))
    (package
      (name "r-cellchat")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/sqjin/CellChat")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0cvzl9mi8jjznpql2gv67swnk1dndn3a2h22z5l84h7lwpwjmh53"))
         (snippet
          '(for-each delete-file '("src/CellChat.so"
                                   "src/CellChat_Rcpp.o"
                                   "src/RcppExports.o")))))
      (properties `((upstream-name . "CellChat")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocgenerics
             r-circlize
             r-colorspace
             r-complexheatmap
             r-cowplot
             r-dplyr
             r-expm
             r-fnn
             r-forcats
             r-future
             r-future-apply
             r-gg-gap
             r-ggalluvial
             r-ggplot2
             r-ggrepel
             r-igraph
             r-irlba
             r-magrittr
             r-matrix
             r-nmf
             r-patchwork
             r-pbapply
             r-rcolorbrewer
             r-rcpp
             r-rcppeigen
             r-reshape2
             r-reticulate
             r-rspectra
             r-rtsne
             r-scales
             r-shape
             r-sna
             r-stringr
             r-svglite))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/sqjin/CellChat")
      (synopsis "Analysis of cell-cell communication from single-cell transcriptomics data")
      (description
       "This package infers, visualizes and analyzes the cell-cell
communication networks from scRNA-seq data.")
      (license license:gpl3))))

(define-public r-cellchat-2
  (let ((commit "b05405af0f4f2cac99f2211e888d42de4c5a9d59")
        (revision "1"))
    (package
      (name "r-cellchat")
      (version (git-version "2.1.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/jinworks/CellChat")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "14s7bl70xi21ivqr1c3qx6kjf1ndlyxag880xldqkfsqpksvyvkc"))
         (snippet '(for-each delete-file
                             '("src/CellChat.so" "src/CellChat_Rcpp.o"
                               "src/RcppExports.o")))))
      (properties `((upstream-name . "CellChat")))
      (build-system r-build-system)
      (propagated-inputs (list r-biocgenerics
                               r-biocneighbors
                               r-bslib
                               r-circlize
                               r-colorspace
                               r-complexheatmap
                               r-cowplot
                               r-dplyr
                               r-fnn
                               r-future
                               r-future-apply
                               r-ggalluvial
                               r-ggnetwork
                               r-ggplot2
                               r-ggpubr
                               r-ggrepel
                               r-igraph
                               r-irlba
                               r-magrittr
                               r-matrix
                               r-nmf
                               r-patchwork
                               r-pbapply
                               r-plotly
                               r-plyr
                               r-rcolorbrewer
                               r-rcpp
                               r-rcppeigen
                               r-reshape2
                               r-reticulate
                               r-rspectra
                               r-scales
                               r-shape
                               r-shiny
                               r-sna
                               r-stringr
                               r-svglite))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/jinworks/CellChat")
      (synopsis
       "Inference of cell-cell communication from single-cell and transcriptomics")
      (description
       "This R tool infers, visualizes, and analyzes cell-cell communication networks.
It supports scRNA-seq and spatially resolved transcriptomics data.")
      (license license:gpl3))))

(define-public r-copykat
  (let ((commit                         ;no tag
         "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53")
        (revision "0"))
    (package
      (name "r-copykat")
      (version (git-version "1.0.8" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/navinlabcode/copykat")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8"))))
      (properties `((upstream-name . "copykat")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-cluster
             r-dlm
             r-gplots
             r-mcmcpack
             r-mixtools
             r-paralleldist
             r-rcolorbrewer))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/navinlabcode/copykat")
      (synopsis "Inference of genomic copy number from single cell RNAseq data")
      (description
       "This package Copynumber KAryotyping of Tumors infers genomic copy
number and subclonal structure of human tumors using integrative Bayesian
approaches to identify genome-wide aneuploidy at 5MB resolution in single
cells data.  It separates tumor cells and tumor subclones from normal cells
using high-throughput sc-RNAseq data.")
      (license license:gpl2))))

(define-public sambamba
  (package
    (name "sambamba")
    (version "0.8.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/biod/sambamba")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1zdkd1md5wk4la71p82pbclqqcm55abk23fk087da6186i1bsihl"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; there is no test target
       #:parallel-build? #f             ; not supported
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (add-after 'unpack 'prepare-build-tools
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "Makefile"
               (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
             (setenv "CC" "gcc")
             (setenv "D_LD" (which "ld.gold"))))
         (add-after 'unpack 'unbundle-prerequisites
           (lambda _
             (substitute* "Makefile"
               (("= lz4/lib/liblz4.a") "= -L-llz4")
               (("ldc_version_info lz4-static") "ldc_version_info"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (mkdir-p bin)
               (copy-file (string-append "bin/sambamba-" ,version)
                          (string-append bin "/sambamba"))))))))
    (native-inputs
     (list python))
    (inputs
     (list ldc lz4 zlib))
    (home-page "https://github.com/biod/sambamba")
    (synopsis "Tools for working with SAM/BAM data")
    (description "Sambamba is a high performance modern robust and
fast tool (and library), written in the D programming language, for
working with SAM and BAM files.  Current parallelised functionality is
an important subset of samtools functionality, including view, index,
sort, markdup, and depth.")
    (license license:gpl2+)))

(define-public r-rphyloxml
  (let ((commit "a30e39249239b2de01d6964ae2a2205a6c48b475")
        (revision "1"))
    (package
      (name "r-rphyloxml")
      (version (git-version "0.0-9000" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/USCbiostats/rphyloxml")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "15ijzqvjxx6vqyqlg5asdbqlhw1g0ix6palf1rism3si0qapddgw"))
         (snippet
          '(delete-file "docs/jquery.sticky-kit.min.js"))))
      (properties `((upstream-name . "rphyloxml")))
      (build-system r-build-system)
      (arguments
       (list
        #:modules
        '((guix build r-build-system)
          (guix build minify-build-system)
          (guix build utils))
        #:imported-modules
        `(,@%r-build-system-modules (guix build minify-build-system))
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'process-javascript
             (lambda* (#:key inputs #:allow-other-keys)
               (with-directory-excursion "inst/"
                 (minify (assoc-ref inputs "js-jquery-sticky-kit")
                         #:target "docs/jquery.sticky-kit.min.js")))))))
      (propagated-inputs (list r-ape r-xml2))
      (native-inputs
       `(("esbuild" ,esbuild)
         ("js-jquery-sticky-kit"
          ,(origin
             (method url-fetch)
             (uri "https://raw.githubusercontent.com/leafo/sticky-kit/\
v1.1.2/jquery.sticky-kit.js")
             (sha256
              (base32
               "17c3a1hqc3ybwj7hpw8prazajp2x98aq7nyfn71h6lzjvblq297g"))))))
      (home-page "https://github.com/USCbiostats/rphyloxml")
      (synopsis "Read and write phyloXML files in R")
      (description
       "The package reads phylogenetic data in the @code{phyloXML} format.
It also includes functions for writing data in this format.")
      (license license:expat))))

(define-public ritornello
  (package
    (name "ritornello")
    (version "2.0.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/KlugerLab/Ritornello")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; there are no tests
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-samtools-references
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* '("src/SamStream.h"
                            "src/FLD.cpp")
               (("<sam.h>") "<samtools/sam.h>"))
             #t))
         (delete 'configure)
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out    (assoc-ref outputs "out"))
                    (bin    (string-append out "/bin/")))
               (mkdir-p bin)
               (install-file "bin/Ritornello" bin)
               #t))))))
    (inputs
     (list samtools-0.1 fftw boost zlib))
    (home-page "https://github.com/KlugerLab/Ritornello")
    (synopsis "Control-free peak caller for ChIP-seq data")
    (description "Ritornello is a ChIP-seq peak calling algorithm based on
signal processing that can accurately call binding events without the need to
do a pair total DNA input or IgG control sample.  It has been tested for use
with narrow binding events such as transcription factor ChIP-seq.")
    (license license:gpl3+)))

(define-public trim-galore
  (package
    (name "trim-galore")
    (version "0.6.6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/FelixKrueger/TrimGalore")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0yrwg6325j4sb9vnplvl3jplzab0qdhp92wl480qjinpfq88j4rs"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; no tests
       #:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda _
             ;; Trim Galore tries to figure out what version of Python
             ;; cutadapt is using by looking at the shebang.  Of course that
             ;; doesn't work, because cutadapt is wrapped in a shell script.
             (substitute* "trim_galore"
               (("my \\$python_return.*")
                "my $python_return = \"Python 3.999\";\n"))
             #t))
         (delete 'build)
         (add-after 'unpack 'hardcode-tool-references
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "trim_galore"
               (("\\$path_to_cutadapt = 'cutadapt'")
                (string-append "$path_to_cutadapt = '"
                               (assoc-ref inputs "cutadapt")
                               "/bin/cutadapt'"))
               (("\\$compression_path = \"gzip\"")
                (string-append "$compression_path = \""
                               (assoc-ref inputs "gzip")
                               "/bin/gzip\""))
               (("\"gunzip")
                (string-append "\""
                               (assoc-ref inputs "gzip")
                               "/bin/gunzip"))
               (("\"pigz")
                (string-append "\""
                               (assoc-ref inputs "pigz")
                               "/bin/pigz")))
             #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out")
                                       "/bin")))
               (mkdir-p bin)
               (install-file "trim_galore" bin)
               #t))))))
    (inputs
     (list gzip perl pigz cutadapt))
    (native-inputs
     (list unzip))
    (home-page "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
    (synopsis "Wrapper around Cutadapt and FastQC")
    (description "Trim Galore! is a wrapper script to automate quality and
adapter trimming as well as quality control, with some added functionality to
remove biased methylation positions for RRBS sequence files.")
    (license license:gpl3+)))

(define-public phylip
  (package
    (name "phylip")
    (version "3.697")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://evolution.gs.washington.edu/phylip/"
                           "download/phylip-" version ".tar.gz"))
       (sha256
        (base32
         "1h8h0nafnlbqryswxgplx80k2044yhfz97jh13vsgzlaifqdh9ls"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; no check target
       #:make-flags (list "-f" "Makefile.unx" "CFLAGS=-fcommon" "install")
       #:parallel-build? #f             ; not supported
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-dir
           (lambda _ (chdir "src")))
         (delete 'configure)
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((target (string-append (assoc-ref outputs "out")
                                          "/bin")))
               (mkdir-p target)
               (for-each (lambda (file)
                           (install-file file target))
                         (find-files "../exe" ".*"))))))))
    (home-page "https://evolution.genetics.washington.edu/phylip/")
    (synopsis "Tools for inferring phylogenies")
    (description "PHYLIP (the PHYLogeny Inference Package) is a package of
programs for inferring phylogenies (evolutionary trees).")
    (license license:bsd-2)))

(define-public phyml
  (package
    (name "phyml")
    (version "3.3.20220408")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/stephaneguindon/phyml")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa"))
              (snippet
               '(delete-file "doc/phyml-manual.pdf"))))
    (build-system gnu-build-system)
    (supported-systems '("x86_64-linux"))
    (arguments
     (let ((default-flags (list "--disable-native")))
       `(#:phases
         (let ((build (lambda (what)
                         (lambda args
                           (apply (assoc-ref %standard-phases 'configure)
                                  (append args
                                          (list #:configure-flags
                                                (cons (format #false "--enable-~a" what)
                                                      '() #;,default-flags))))
                           (apply (assoc-ref %standard-phases 'build) args)
                           (apply (assoc-ref %standard-phases 'install) args)))))
           (modify-phases %standard-phases
             ;; We cannot use --disable-native; see
             ;; https://github.com/stephaneguindon/phyml/issues/173 Instead we
             ;; patch the code to at least get rid of -march=native.
             (add-after 'unpack 'remove-march-native
               (lambda _
                 (substitute* "configure.ac"
                   (("DEFAULT_VECTOR_FLAG=\"-march=native\"")
                    "DEFAULT_VECTOR_FLAG=\"-march=athlon64-sse3\"\n"))))
             (add-after 'build 'build-manual
               (lambda _
                 (with-directory-excursion "doc"
                   (invoke "make" "phyml-manual.pdf"))))
             (add-after 'build-manual 'install-manual
               (lambda* (#:key outputs #:allow-other-keys)
                 (with-directory-excursion "doc"
                   (install-file "phyml-manual.pdf"
                                 (string-append (assoc-ref outputs "out")
                                                "/share/doc/phyml")))))
             (add-after 'install 'build-phyml-mpi
               (build "phyml-mpi"))
             (add-after 'build-phyml-mpi 'build-rf
               (build "rf"))
             (add-after 'build-rf 'build-phyrex
               (build "phyrex")))))))
    (native-inputs
     (list automake
           autoconf
           openmpi
           (texlive-updmap.cfg
            (list texlive-caption
                  texlive-cite
                  texlive-fancyvrb
                  texlive-infwarerr
                  texlive-kvoptions
                  texlive-pdftexcmds
                  texlive-psfrag
                  texlive-xcolor))))
    (home-page "https://github.com/stephaneguindon/phyml")
    (synopsis "Programs for working on SAM/BAM files")
    (description
     "@code{PhyML} is a software package that uses modern statistical
approaches to analyse alignments of nucleotide or amino acid sequences in a
phylogenetic framework.  The main tool in this package builds phylogenies
under the maximum likelihood criterion.  It implements a large number of
substitution models coupled with efficient options to search the space of
phylogenetic tree topologies.  code{PhyREX} fits the
spatial-Lambda-Fleming-Viot model to geo-referenced genetic data.  This model
is similar to the structured coalescent but assumes that individuals are
distributed along a spatial continuum rather than discrete demes.
@code{PhyREX} can be used to estimate population densities and rates of
dispersal.  Its output can be processed by treeannotator (from the
@code{BEAST} package) as well as @code{SPREAD}.")
    (license license:gpl3)))

(define-public imp
  (package
    (name "imp")
    (version "2.15.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://integrativemodeling.org/"
                           version "/download/imp-" version ".tar.gz"))
       (sha256
        (base32
         "05hsrnkpkajppa3f45x4qsarnkj616hlby749zxg4is3bv4i6b5y"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #false ; The test suite is notoriously fickle
       #:configure-flags
       (let ((disabled-tests
              '("expensive"                 ;exclude expensive tests
                "IMP.modeller"              ;fail to import its own modules
                "IMP.parallel-test_sge.py"  ;fail in build container
                ;; The following test fails non-reproducibly on
                ;; an inexact numbers assertion.
                "IMP.em-medium_test_local_fitting.py"
                ;; The following test fails for unknown reasons
                "IMP.foxs-add-missing-residues.py")))
         (list
          (string-append
           "-DCMAKE_CTEST_ARGUMENTS="
           (string-join
            (list "-L" "-tests?-"       ;select only tests
                  "-E" (format #f "'(~a)'" (string-join disabled-tests "|")))
            ";"))))))
    (native-inputs
     `(("python" ,python-wrapper)
       ("swig" ,swig)))
    (inputs
     (list boost
           cgal
           gsl
           hdf5
           fftw
           eigen
           ;; Enabling MPI causes the build to use all the available memory and
           ;; fail (tested on a machine with 32 GiB of RAM).
           ;;("mpi" ,openmpi)
           opencv))
    (propagated-inputs
     (list python-numpy python-scipy python-pandas python-scikit-learn
           python-networkx))
    (home-page "https://integrativemodeling.org")
    (synopsis "Integrative modeling platform")
    (description "IMP's broad goal is to contribute to a comprehensive
structural characterization of biomolecules ranging in size and complexity
from small peptides to large macromolecular assemblies, by integrating data
from diverse biochemical and biophysical experiments.  IMP provides a C++ and
Python toolbox for solving complex modeling problems, and a number of
applications for tackling some common problems in a user-friendly way.")
    ;; IMP is largely available under the GNU Lesser GPL; see the file
    ;; COPYING.LGPL for the full text of this license. Some IMP modules are
    ;; available under the GNU GPL (see the file COPYING.GPL).
    (license (list license:lgpl2.1+
                   license:gpl3+))))

;; We use this seemingly arbitrary commit because of
;; https://github.com/3DGenomes/TADbit/issues/371
(define-public tadbit
  (let ((commit "283812901a00078c725bd9f0ee33366af6783969")
        (revision "2"))
    (package
      (name "tadbit")
      (version (git-version "1.0.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/3DGenomes/TADbit")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "07q0alxah6xl1hibaj1kj7pdzq3pg6csyapsihbwlbmqyfmllbgz"))))
      (build-system python-build-system)
      (arguments
       (list
        #:phases
        #~(modify-phases %standard-phases
            ;; Scipy 1.12 no longer has binom_test or polyfit
            (add-after 'unpack 'scipy-compatibility
              (lambda _
                (substitute* '("_pytadbit/modelling/imp_modelling.py"
                               "_pytadbit/modelling/restraints.py")
                  (("from scipy .*import polyfit")
                   "from numpy import polyfit"))
                (substitute* "_pytadbit/mapping/restriction_enzymes.py"
                  (("from scipy.stats import binom_test")
                   "from scipy.stats import binomtest")
                  (("binom_test\\(pats[k]['count'], nreads, 0.25\\*\\*len\\(k\\), alternative='greater'\\)")
                   "binomtest(pats[k]['count'], nreads, 0.25**len(k), alternative='greater').pval"))))
            (add-after 'unpack 'fix-problems-with-setup.py
              (lambda _
                (substitute* "src/test/Makefile"
                  (("^CFLAGS=") "CFLAGS= -fcommon"))

                ;; Don't attempt to install the bash completions to
                ;; the home directory.
                (rename-file "extras/.bash_completion"
                             "extras/tadbit")
                (substitute* "setup.py"
                  (("\\(path.expanduser\\('~'\\)")
                   (string-append "(\"" #$output
                                  "/etc/bash_completion.d\""))
                  (("extras/\\.bash_completion")
                   "extras/tadbit"))))
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys)
                (when tests?
                  (invoke "python3" "test/test_all.py")))))))
      (native-inputs
       (list `(,glib "bin") ;for gtester
             glib
             pkg-config))
      (inputs
       ;; TODO: add Chimera for visualization
       (list imp
             mcl
             python-future
             python-h5py
             python-scipy
             python-numpy
             python-matplotlib
             python-pysam
             r-minimal))
      (home-page "https://3dgenomes.github.io/TADbit/")
      (synopsis "Analyze, model, and explore 3C-based data")
      (description
       "TADbit is a complete Python library to deal with all steps to analyze,
model, and explore 3C-based data.  With TADbit the user can map FASTQ files to
obtain raw interaction binned matrices (Hi-C like matrices), normalize and
correct interaction matrices, identify and compare the so-called
@dfn{Topologically Associating Domains} (TADs), build 3D models from the
interaction matrices, and finally, extract structural properties from the
models.  TADbit is complemented by TADkit for visualizing 3D models.")
      (license license:gpl3+))))

(define-public kentutils
  (package
    (name "kentutils")
    ;; 302.1.0 is out, but the only difference is the inclusion of
    ;; pre-built binaries.
    (version "302.0.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/ENCODE-DCC/kentUtils")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
       (modules '((guix build utils)
                  (srfi srfi-26)
                  (ice-9 ftw)))
       (snippet
        '(begin
           ;; Only the contents of the specified directories are free
           ;; for all uses, so we remove the rest.  "hg/autoSql" and
           ;; "hg/autoXml" are nominally free, but they depend on a
           ;; library that is built from the sources in "hg/lib",
           ;; which is nonfree.
           (let ((free (list "." ".."
                             "utils" "lib" "inc" "tagStorm"
                             "parasol" "htslib"))
                 (directory? (lambda (file)
                               (eq? 'directory (stat:type (stat file))))))
             (for-each (lambda (file)
                         (and (directory? file)
                              (delete-file-recursively file)))
                       (map (cut string-append "src/" <>)
                            (scandir "src"
                                     (lambda (file)
                                       (not (member file free)))))))
           ;; Only make the utils target, not the userApps target,
           ;; because that requires libraries we won't build.
           (substitute* "Makefile"
             ((" userApps") " utils"))
           ;; Only build libraries that are free.
           (substitute* "src/makefile"
             (("DIRS =.*") "DIRS =\n")
             (("cd jkOwnLib.*") "")
             ((" hgLib") "")
             (("cd hg.*") ""))
           (substitute* "src/utils/makefile"
             ;; These tools depend on "jkhgap.a", which is part of the
             ;; nonfree "src/hg/lib" directory.
             (("raSqlQuery") "")
             (("pslLiftSubrangeBlat") "")

             ;; Do not build UCSC tools, which may require nonfree
             ;; components.
             (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
           #t))))
    (build-system gnu-build-system)
    (arguments
     `( ;; There is no global test target and the test target for
       ;; individual tools depends on input files that are not
       ;; included.
       #:tests? #f
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-permissions
           (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
         (add-after 'unpack 'fix-paths
           (lambda _
             (substitute* "Makefile"
               (("/bin/echo") (which "echo")))
             #t))
         (add-after 'unpack 'prepare-samtabix
           (lambda* (#:key inputs #:allow-other-keys)
             (copy-recursively (assoc-ref inputs "samtabix")
                               "samtabix")
             #t))
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out")
                                       "/bin")))
               (copy-recursively "bin" bin))
             #t)))))
    (native-inputs
     `(("samtabix"
        ,(let ((commit "10fd107909c1ac4d679299908be4262a012965ba"))
           (origin
             (method git-fetch)
             (uri (git-reference
                   (url "http://genome-source.cse.ucsc.edu/samtabix.git")
                   (commit commit)))
             (file-name (git-file-name "samtabix" (string-take commit 7)))
             (sha256
              (base32
               "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))))
    (inputs
     `(("zlib" ,zlib)
       ("tcsh" ,tcsh)
       ("perl" ,perl)
       ("libpng" ,libpng)
       ("mariadb-dev" ,mariadb "dev")
       ("openssl" ,openssl)))
    (home-page "https://genome.cse.ucsc.edu/index.html")
    (synopsis "Assorted bioinformatics utilities")
    (description "This package provides the kentUtils, a selection of
bioinformatics utilities used in combination with the UCSC genome
browser.")
    ;; Only a subset of the sources are released under a non-copyleft
    ;; free software license.  All other sources are removed in a
    ;; snippet.  See this bug report for an explanation of how the
    ;; license statements apply:
    ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
    (license (license:non-copyleft
              "http://genome.ucsc.edu/license/"
              "The contents of this package are free for all uses."))))

(define-public f-seq
  (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
        (revision "1"))
    (package
      (name "f-seq")
      (version (git-version "1.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/aboyle/F-seq")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
                (modules '((guix build utils)))
                ;; Remove bundled Java library archives.
                (snippet
                 '(for-each delete-file (find-files "lib" ".*")))))
      (build-system ant-build-system)
      (arguments
       `(#:tests? #f ; no tests included
         #:phases
         (modify-phases %standard-phases
           (replace 'install
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let* ((target (assoc-ref outputs "out"))
                      (bin (string-append target "/bin"))
                      (doc (string-append target "/share/doc/f-seq"))
                      (lib (string-append target "/lib")))
                 (mkdir-p target)
                 (mkdir-p doc)
                 (substitute* "bin/linux/fseq"
                   (("java") (which "java"))
                   (("\\$REALDIR/../lib/commons-cli-1.1.jar")
                    (search-input-file inputs
                                       (string-append "/lib/m2/commons-cli/commons-cli/"
                                                      ,(package-version java-commons-cli)
                                                      "/commons-cli-"
                                                      ,(package-version java-commons-cli)
                                                      ".jar")))
                   (("REALDIR=.*")
                    (string-append "REALDIR=" bin "\n")))
                 (install-file "README.txt" doc)
                 (install-file "bin/linux/fseq" bin)
                 (install-file "build~/fseq.jar" lib)
                 (copy-recursively "lib" lib)))))))
      (inputs
       (list perl java-commons-cli))
      (home-page "https://fureylab.web.unc.edu/software/fseq/")
      (synopsis "Feature density estimator for high-throughput sequence tags")
      (description
       "F-Seq is a software package that generates a continuous tag sequence
density estimation allowing identification of biologically meaningful sites
such as transcription factor binding sites (ChIP-seq) or regions of open
chromatin (DNase-seq).  Output can be displayed directly in the UCSC Genome
Browser.")
      (license license:gpl3+))))

(define-public bismark
  (package
    (name "bismark")
    (version "0.24.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/FelixKrueger/Bismark")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0j4dy33769f0jr2w1brb710zxwpg3zwjlnvlcpi5pr6mqc8dkg8n"))
       (snippet '(delete-file "plotly/plot.ly"))))
    (build-system perl-build-system)
    (arguments
     (list
      #:tests? #f                       ; there are no tests
      #:modules '((guix build utils)
                  (ice-9 popen)
                  (srfi srfi-26)
                  (guix build perl-build-system))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'replace-plotly.js
            (lambda* (#:key inputs #:allow-other-keys)
              (let* ((share (string-append #$output "/share/bismark"))
                     (file (assoc-ref inputs "plotly.js"))
                     (installed "plotly/plotly.js"))
                ;; The bundled plotly.js is minified.
                (let ((minified (open-pipe* OPEN_READ "uglifyjs" file)))
                  (call-with-output-file installed
                    (cut dump-port minified <>)))
                (substitute* "bismark2report"
                  (("plotly_template.tpl")
                   (string-append share "/plotly/plotly_template.tpl"))
                  (("my \\$plotly_code = read_report_template\\('plot.ly'\\);")
                   (string-append "\
my $plotly_code = read_report_template('" share "/plotly/plotly.js');
$plotly_code = \"<script>\" . $plotly_code . \"</script>\";"))))))
          (replace 'configure
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "bismark"
                (("\\(\\!system \"which samtools >/dev/null 2>&1\"\\)")
                 "(\"true\")")
                (("\\$samtools_path = `which samtools`;")
                 (string-append "$samtools_path = '"
                                (search-input-file inputs "/bin/samtools")
                                "';"))
                (("\\$path_to_bowtie2 = 'bowtie2'")
                 (string-append "$path_to_bowtie2 = '"
                                (search-input-file inputs "/bin/bowtie2")
                                "'"))
                (("\\$path_to_hisat2 = 'hisat2'")
                 (string-append "$path_to_hisat2 = '"
                                (search-input-file inputs "/bin/hisat2")
                                "'"))
                (("\\$path_to_minimap2 = 'minimap2'")
                 (string-append "$path_to_minimap2 = '"
                                (search-input-file inputs "/bin/minimap2")
                                "'")))))
          (delete 'build)
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((bin (string-append #$output "/bin"))
                     (share   (string-append #$output "/share/bismark"))
                     (docdir  (string-append #$output "/share/doc/bismark"))
                     (scripts '("bismark"
                                "bismark_genome_preparation"
                                "bismark_methylation_extractor"
                                "bismark2bedGraph"
                                "bismark2report"
                                "coverage2cytosine"
                                "deduplicate_bismark"
                                "filter_non_conversion"
                                "bam2nuc"
                                "bismark2summary"
                                "NOMe_filtering")))
                (mkdir-p share)
                (mkdir-p docdir)
                (mkdir-p bin)
                (for-each (lambda (file) (install-file file bin))
                          scripts)
                (copy-recursively "docs" docdir)
                (copy-recursively "plotly"
                                  (string-append share "/plotly"))

                ;; Fix references to gunzip
                (substitute* (map (lambda (file)
                                    (string-append bin "/" file))
                                  scripts)
                  (("\"gunzip -c")
                   (string-append "\"" (assoc-ref inputs "gzip")
                                  "/bin/gunzip -c")))))))))
    (inputs
     (list bowtie gzip hisat2 minimap2 perl-carp perl-getopt-long samtools))
    (native-inputs
     `(("plotly.js"
        ,(origin
           (method url-fetch)
           (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/"
                               "v1.39.4/dist/plotly.js"))
           (sha256
            (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
       ("uglifyjs" ,node-uglify-js)))
    (home-page "https://www.bioinformatics.babraham.ac.uk/projects/bismark/")
    (synopsis "Map bisulfite treated sequence reads and analyze methylation")
    (description "Bismark is a program to map bisulfite treated sequencing
reads to a genome of interest and perform methylation calls in a single step.
The output can be easily imported into a genome viewer, such as SeqMonk, and
enables a researcher to analyse the methylation levels of their samples
straight away.  Its main features are:

@itemize
@item Bisulfite mapping and methylation calling in one single step
@item Supports single-end and paired-end read alignments
@item Supports ungapped and gapped alignments
@item Alignment seed length, number of mismatches etc are adjustable
@item Output discriminates between cytosine methylation in CpG, CHG
  and CHH context
@end itemize\n")
    (license license:gpl3+)))

(define-public paml
  (package
    (name "paml")
    (version "4.9e")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
                                  "paml" version ".tgz"))
              (sha256
               (base32
                "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
              (modules '((guix build utils)))
              ;; Remove Windows binaries
              (snippet
               '(begin
                  (for-each delete-file (find-files "." "\\.exe$"))
                  ;; Some files in the original tarball have restrictive
                  ;; permissions, which makes repackaging fail
                  (for-each (lambda (file) (chmod file #o644)) (find-files "."))
                  #t))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; there are no tests
       #:make-flags '("CC=gcc" "CFLAGS=-fcommon -O3")
       #:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda _
             (substitute* "src/BFdriver.c"
               (("/bin/bash") (which "bash")))
             (chdir "src")))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((tools '("baseml" "basemlg" "codeml"
                            "pamp" "evolver" "yn00" "chi2"))
                   (bin    (string-append (assoc-ref outputs "out") "/bin"))
                   (docdir (string-append (assoc-ref outputs "out")
                                           "/share/doc/paml")))
               (mkdir-p bin)
               (for-each (lambda (file) (install-file file bin)) tools)
               (copy-recursively "../doc" docdir)))))))
    (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
    (synopsis "Phylogentic analysis by maximum likelihood")
    (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
contains a few programs for model fitting and phylogenetic tree reconstruction
using nucleotide or amino-acid sequence data.")
    ;; GPLv3 only
    (license license:gpl3)))

(define-public segemehl
  (package
    (name "segemehl")
    (version "0.3.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.bioinf.uni-leipzig.de/Software"
                                  "/segemehl/downloads/segemehl-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0lbzbb7i8zadsn9b99plairhq6s2h1z8qdn6n7djclfis01nycz4"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (list (string-append "CC=" ,(cc-for-target))
             "all")
       #:tests? #false ; there are none
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         ;; There is no installation target
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out  (assoc-ref outputs "out"))
                    (bin  (string-append out "/bin"))
                    (exes (list "segemehl.x" "haarz.x")))
               (mkdir-p bin)
               (for-each (lambda (exe)
                           (install-file exe bin))
                         exes)))))))
    (inputs
     (list htslib ncurses zlib))
    (native-inputs
     (list pkg-config))
    (home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl")
    (synopsis "Map short sequencer reads to reference genomes")
    (description "Segemehl is software to map short sequencer reads to
reference genomes.  Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA).  It accepts fasta and fastq queries (gzip'ed and
bgzip'ed).  In addition to the alignment of reads from standard DNA- and
RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.  The
output of segemehl is a SAM or BAM formatted alignment file.")
    (license license:gpl3+)))

(define-public kallisto
  (package
    (name "kallisto")
    (version "0.50.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/pachterlab/kallisto")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0zfs79mv75599cf9d7d3c5a3s8idgz9qvl4qfzhvhbd87y3dv7p0"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:tests? #false          ;no "check" target
      ;; The build system attempts to link libbifrost.a into the kallisto
      ;; executable before the library has been built.
      #:parallel-build? #false))
    (inputs (list hdf5 zlib))
    (home-page "https://pachterlab.github.io/kallisto/")
    (synopsis "Near-optimal RNA-Seq quantification")
    (description
     "Kallisto is a program for quantifying abundances of transcripts from
RNA-Seq data, or more generally of target sequences using high-throughput
sequencing reads.  It is based on the novel idea of pseudoalignment for
rapidly determining the compatibility of reads with targets, without the need
for alignment.  Pseudoalignment of reads preserves the key information needed
for quantification, and kallisto is therefore not only fast, but also as
accurate as existing quantification tools.")
    (license license:bsd-2)))

(define-public libgff
  (package
    (name "libgff")
    (version "2.0.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/COMBINE-lab/libgff")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0ds9r22y8bl1rj7bhl0003kgmm6aam7g8l41mnjfrzw15d9zf9k4"))))
    (build-system cmake-build-system)
    (arguments `(#:tests? #f))          ; no tests included
    (home-page "https://github.com/COMBINE-lab/libgff")
    (synopsis "Parser library for reading/writing GFF files")
    (description "This is a simple \"libraryfication\" of the GFF/GTF parsing
code that is used in the Cufflinks codebase.  The goal of this library is to
provide this functionality without the necessity of drawing in a heavy-weight
dependency like SeqAn.")
    (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))

(define-public sailfish
  (package
    (name "sailfish")
    (version "0.10.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/kingsfordgroup/sailfish")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
              (modules '((guix build utils)))
              ;; Delete bundled headers for eigen3.
              (snippet
               '(delete-file-recursively "include/eigen3/"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       ,#~(list (string-append "-DBOOST_INCLUDEDIR="
                               #$(this-package-input "boost")
                               "/include/")
                (string-append "-DBOOST_LIBRARYDIR="
                               #$(this-package-input "boost")
                               "/lib/")
                (string-append "-DBoost_LIBRARIES="
                               "-lboost_iostreams "
                               "-lboost_filesystem "
                               "-lboost_system "
                               "-lboost_thread "
                               "-lboost_timer "
                               "-lboost_chrono "
                               "-lboost_program_options")
                "-DBoost_FOUND=TRUE"
                ;; Don't download RapMap---we already have it!
                "-DFETCHED_RAPMAP=1")
       ;; Tests must be run after installation and the location of the test
       ;; data file must be overridden.  But the tests fail.  It looks like
       ;; they are not really meant to be run.
       #:tests? #f
       #:phases
       (modify-phases %standard-phases
         ;; Boost cannot be found, even though it's right there.
         (add-after 'unpack 'do-not-look-for-boost
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "CMakeLists.txt"
               (("find_package\\(Boost 1\\.53\\.0") "#"))))
         (add-after 'unpack 'do-not-assign-to-macro
           (lambda _
             (substitute* "include/spdlog/details/format.cc"
               (("const unsigned CHAR_WIDTH = 1;") ""))))
         (add-after 'unpack 'prepare-rapmap
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((src "external/install/src/rapmap/")
                   (include "external/install/include/rapmap/")
                   (rapmap (assoc-ref inputs "rapmap")))
               (mkdir-p src)
               (mkdir-p include)
               (for-each (lambda (file)
                           (install-file file src))
                         (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
               (copy-recursively (string-append rapmap "/include") include))))
         (add-after 'unpack 'use-system-libraries
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* '("src/SailfishIndexer.cpp"
                            "src/SailfishUtils.cpp"
                            "src/SailfishQuantify.cpp"
                            "src/FASTAParser.cpp"
                            "include/PCA.hpp"
                            "include/SailfishUtils.hpp"
                            "include/SailfishIndex.hpp"
                            "include/CollapsedEMOptimizer.hpp"
                            "src/CollapsedEMOptimizer.cpp")
               (("#include \"jellyfish/config.h\"") ""))
             (substitute* "src/CMakeLists.txt"
               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
                (search-input-directory
                 inputs
                 (string-append "/include/jellyfish-" ,(package-version jellyfish))))
               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
                (search-input-file inputs
                                   "/lib/libjellyfish-2.0.a"))
               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
                (search-input-file inputs
                                   "/lib/libdivsufsort.so"))
               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
                (search-input-file inputs
                                   "/lib/libdivsufsort64.so")))
             (substitute* "CMakeLists.txt"
               ;; Don't prefer static libs
               (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
               (("find_package\\(Jellyfish.*") "")
               (("ExternalProject_Add\\(libjellyfish") "message(")
               (("ExternalProject_Add\\(libgff") "message(")
               (("ExternalProject_Add\\(libsparsehash") "message(")
               (("ExternalProject_Add\\(libdivsufsort") "message("))

             ;; Ensure that Eigen headers can be found
             (setenv "CPLUS_INCLUDE_PATH"
                     (string-append (search-input-directory
                                     inputs "/include/eigen3")
                                    ":"
                                    (or (getenv "CPLUS_INCLUDE_PATH") ""))))))))
    (inputs
     `(("boost" ,boost)
       ("eigen" ,eigen)
       ("jemalloc" ,jemalloc)
       ("jellyfish" ,jellyfish)
       ("sparsehash" ,sparsehash)
       ("rapmap" ,(origin
                    (method git-fetch)
                    (uri (git-reference
                          (url "https://github.com/COMBINE-lab/RapMap")
                          (commit (string-append "sf-v" version))))
                    (file-name (string-append "rapmap-sf-v" version "-checkout"))
                    (sha256
                     (base32
                      "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
                    (modules '((guix build utils)))
                    ;; These files are expected to be excluded.
                    (snippet
                     '(begin (delete-file-recursively "include/spdlog")
                             (for-each delete-file '("include/xxhash.h"
                                                     "src/xxhash.c"))))))
       ("libdivsufsort" ,libdivsufsort)
       ("libgff" ,libgff)
       ("tbb" ,tbb-2020)
       ("zlib" ,zlib)))
    (native-inputs
     (list pkg-config))
    (home-page "https://www.cs.cmu.edu/~ckingsf/software/sailfish/")
    (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
    (description "Sailfish is a tool for genomic transcript quantification
from RNA-seq data.  It requires a set of target transcripts (either from a
reference or de-novo assembly) to quantify.  All you need to run sailfish is a
fasta file containing your reference transcripts and a (set of) fasta/fastq
file(s) containing your reads.")
    (license license:gpl3+)))

(define libstadenio-for-salmon
  (package
    (name "libstadenio")
    (version "1.14.8")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/COMBINE-lab/staden-io_lib")
                    (commit (string-append "v" version))))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
    (build-system gnu-build-system)
    (arguments '(#:parallel-tests? #f)) ; not supported
    (inputs
     `(("zlib" ,zlib)))
    (native-inputs
     `(("perl" ,perl)))                 ; for tests
    (home-page "https://github.com/COMBINE-lab/staden-io_lib")
    (synopsis "General purpose trace and experiment file library")
    (description "This package provides a library of file reading and writing
code to provide a general purpose Trace file (and Experiment File) reading
interface.

The following file formats are supported:

@enumerate
@item SCF trace files
@item ABI trace files
@item ALF trace files
@item ZTR trace files
@item SFF trace archives
@item SRF trace archives
@item Experiment files
@item Plain text files
@item SAM/BAM sequence files
@item CRAM sequence files
@end enumerate\n")
    (license license:bsd-3)))

(define-public salmon
  (package
    (name "salmon")
    (version "1.10.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/COMBINE-lab/salmon")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0grpcajxf2bch4b74zb66pdssda8yc7jvxj5ckaw0xvw1605rpcj"))
              (modules '((guix build utils)))
              (snippet
               ;; Delete bundled headers for eigen3.
               '(delete-file-recursively "include/eigen3/"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      #~(list (string-append "-Dlibgff_DIR="
                             #$(this-package-input "libgff") "/lib")
              "-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\""
              "-Dlibgff_FOUND=TRUE"
              "-DTBB_FOUND=TRUE"
              #$(string-append "-DTBB_VERSION=" (package-version tbb))
              "-DFETCHED_PUFFERFISH=TRUE"
              "-DUSE_SHARED_LIBS=TRUE")
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'prepare-pufferfish
            (lambda* (#:key inputs #:allow-other-keys)
              (copy-recursively (assoc-ref inputs "pufferfish")
                                "external/pufferfish")
              ;; This test isn't working correctly, so compilation aborts.
              (substitute* "external/pufferfish/include/string_view.hpp"
                (("#if __has_include\\(<string_view>\\)")
                 "#if 0"))
              (let ((headers "external/install/pufferfish/include/pufferfish")
                    (source "external/install/src/pufferfish"))
                (mkdir-p headers)
                (mkdir-p source)
                (for-each (lambda (file)
                            (install-file (string-append "external/pufferfish/include/" file)
                                          headers))
                          (list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp"
                                "Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp"
                                "CanonicalKmerIterator.hpp"
                                "PufferfishBaseIndex.hpp"
                                "PufferfishIndex.hpp"
                                "PufferfishSparseIndex.hpp"
                                "PufferfishLossyIndex.hpp"
                                "PufferfishTypes.hpp"
                                "rank9b.hpp" "rank9sel.hpp" "macros.hpp"
                                "select.hpp" "Util.hpp"
                                "PairedAlignmentFormatter.hpp"
                                "SelectiveAlignmentUtils.hpp"
                                "PuffAligner.hpp" "MemCollector.hpp"
                                "MemChainer.hpp" "CommonTypes.hpp"
                                "SAMWriter.hpp" "PufferfishConfig.hpp"
                                "BulkChunk.hpp" "BinWriter.hpp"))

                (for-each (lambda (dir)
                            (copy-recursively
                             (string-append "external/pufferfish/include/" dir)
                             (string-append headers "/" dir)))
                          (list "libdivide"
                                "ksw2pp"
                                "compact_vector"
                                "itlib"
                                "metro"
                                "chobo"
                                "sparsepp"
                                "simde"
                                "tsl"))
                (copy-recursively
                 (string-append "external/pufferfish/src/metro/")
                 (string-append source "/metro"))
                (install-file
                 (string-append "external/pufferfish/src/rank9b.cpp")
                 source)

                ;; Do not complain about not having built libtbb
                (substitute* "external/pufferfish/external/twopaco/CMakeLists.txt"
                  (("add_dependencies.*") "")))))
          (add-after 'unpack 'do-not-phone-home
            (lambda _
              (substitute* "src/Salmon.cpp"
                (("getVersionMessage\\(\\)") "\"\""))))
          (add-after 'unpack 'use-system-libraries
            (lambda* (#:key inputs #:allow-other-keys)
              ;; Ensure that all headers can be found
              (setenv "CPLUS_INCLUDE_PATH"
                      (string-append (or (getenv "CPLUS_INCLUDE_PATH") "")
                                     ":"
                                     (getcwd) "/external/install/pufferfish/include:"
                                     (assoc-ref inputs "eigen")
                                     "/include/eigen3"))))
          (add-after 'unpack 'fix-error-message-in-tests
            (lambda _
              (substitute* "cmake/TestSalmonQuasi.cmake"
                (("SALMON_QUASI_INDEX_COMMAND")
                 "SALMON_QUASI_INDEX_CMD")))))))
    (inputs
     (list boost
           bzip2
           cereal
           curl
           eigen
           htscodecs
           jemalloc
           libgff
           tbb
           libstadenio-for-salmon
           xz
           zlib))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("pufferfish" ,(origin
                        (method git-fetch)
                        (uri (git-reference
                              (url "https://github.com/COMBINE-lab/pufferfish")
                              (commit (string-append "salmon-v" version))))
                        (file-name (git-file-name "pufferfish" version))
                        (sha256
                         (base32
                          "0fcv5rd2k4fabsg489sjfxgjisivhwk1w26gfc88rgpszdkcla36"))))))
    (home-page "https://github.com/COMBINE-lab/salmon")
    (synopsis "Quantification from RNA-seq reads using lightweight alignments")
    (description "Salmon is a program to produce highly-accurate,
transcript-level quantification estimates from RNA-seq data.  Salmon achieves
its accuracy and speed via a number of different innovations, including the
use of lightweight alignments (accurate but fast-to-compute proxies for
traditional read alignments) and massively-parallel stochastic collapsed
variational inference.")
    (license license:gpl3+)))

(define-public scallop
  (package
    (name "scallop")
    (version "0.10.5")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/Kingsford-Group/scallop"
                                  "/releases/download/v" version
                                  "/scallop-" version ".tar.gz"))
              (sha256
               (base32
                "0ylkhr5hsmw7bsdszrjz9yqknsijh2fl5n6rjqmdmcdky5hkr7mh"))))
    (build-system gnu-build-system)
    (inputs
     (list boost htslib))
    (home-page "https://github.com/Kingsford-Group/scallop")
    (synopsis "Reference-based transcriptome assembler for RNA-seq")
    (description "Scallop is a reference-based transcript assembler.  Scallop
features its high accuracy in assembling multi-exon transcripts as well as
lowly expressed transcripts.")
    (license license:bsd-3)))

(define-public python-fanc
  (package
    (name "python-fanc")
    (version "0.9.25")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/vaquerizaslab/fanc")
                    ;; There are no tags.  This commit corresponds to
                    ;; version 0.9.25.
                    (commit "e2205346c13ea5349681dff21adeb271d4ea5261")))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0rxq24p852iiayi0083fyigvc30as695rha71q6xd4s2ij1k9mqi"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "pytest" "-vv"
                       "-k"
                       ;; XXX: These all fail because they fail to read
                       ;; the included test_{cooler,juicer}.hic files.
                       (string-append "not test_edges_iter"
                                      " and not test_get_edges_uncorrected"
                                      " and not test_get_edges"))))))))
    (propagated-inputs
     (list python-biopython
           python-cooler
           python-deprecated
           python-future
           python-genomic-regions
           python-gridmap
           python-h5py
           python-intervaltree
           python-matplotlib
           python-msgpack
           python-msgpack-numpy
           python-numpy
           python-pandas
           python-pillow
           python-progressbar2
           python-pybedtools
           python-pybigwig
           python-pysam
           python-pytest
           python-pyyaml
           python-scikit-image
           python-scikit-learn
           python-scipy
           python-seaborn
           python-tables))
    (native-inputs
     (list python-cython))
    (home-page "https://github.com/vaquerizaslab/fanc")
    (synopsis "Framework for the analysis of C-data")
    (description
     "FAN-C provides a pipeline for analysing Hi-C data starting at
mapped paired-end sequencing reads.")
    (license license:gpl3+)))

(define-public python-genomic-regions
  (package
    (name "python-genomic-regions")
    (version "0.0.10")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "genomic_regions" version))
              (sha256
               (base32
                "0hz811iyd1prml1r90qyzimmwyjwycwkjqw4vnl12bxy61rfzjz5"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-future
           python-intervaltree
           python-numpy
           python-pandas
           python-pybedtools
           python-pybigwig
           python-pytest
           python-msgpack-numpy
           python-cython
           python-msgpack
           python-pysam))
    (home-page "https://pypi.org/project/genomic-regions/")
    (synopsis "Consistently handle genomic regions")
    (description "This package aims to simplify working with genomic region /
interval data by providing a common interface that lets you access a wide
selection of file types and formats for handling genomic region data---all
using the same syntax.")
    (license license:expat)))

(define-public python-goatools
  (package
    (name "python-goatools")
    (version "1.3.1")
    ;; Pypi tarball doesn't include test files.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/tanghaibao/goatools")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0a295zk9jc8kny5vnka63q3gbksins42kcmgvskf8xy7hkca7cmq"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      ;; Almost all tests require access to the internet.
      #:tests? #false
      #:test-flags
      ;; These have syntax errors.
      '(list "--ignore=tests/test_i195_sgd_gaf.py"
             "--ignore=tests/test_i206.py"
             "--ignore=tests/test_setup_dirs.py")))
    (propagated-inputs (list python-docopt
                             python-numpy
                             python-openpyxl
                             python-pandas
                             python-pydot
                             python-requests
                             python-scipy
                             python-statsmodels
                             python-xlsxwriter))
    (native-inputs (list python-pytest))
    (home-page "https://github.com/tanghaibao/goatools")
    (synopsis "Python scripts to find enrichment of GO terms")
    (description "Python scripts to find enrichment of GO terms.  In addition,
this package is used for processing the obo-formatted file from Gene Ontology
website.  The data structure is a directed acyclic graph that allows easy
traversal from leaf to root.")
    (license license:bsd-2)))

(define-public python-loompy
  (package
    (name "python-loompy")
    (version "3.0.7")
    ;; The tarball on Pypi does not include the tests.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linnarsson-lab/loompy")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0xmw2yv1y3y7vh5jcbrmlkn43nmfs0pf6z78k1yxqs3qy248m9b0"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; See https://github.com/linnarsson-lab/loompy/issues/169
         (add-after 'unpack 'fix-h5py-error
           (lambda _
             (substitute* "tests/test_file_attribute_manager.py"
               (("h5py.File\\(f.name\\)")
                "h5py.File(f.name, 'a')"))))
         ;; Numba needs a writable dir to cache functions.
         (add-before 'check 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp")))
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (invoke "pytest" "tests")))))))
    (propagated-inputs
     (list python-click
           python-h5py
           python-numba
           python-numpy
           python-numpy-groupies
           python-pandas
           python-scipy))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/linnarsson-lab/loompy")
    (synopsis "Work with .loom files for single-cell RNA-seq data")
    (description "The loom file format is an efficient format for very large
omics datasets, consisting of a main matrix, optional additional layers, a
variable number of row and column annotations.  Loom also supports sparse
graphs.  This library makes it easy to work with @file{.loom} files for
single-cell RNA-seq data.")
    (license license:bsd-3)))

(define-public python-biothings-client
  (package
    (name "python-biothings-client")
    (version "0.2.6")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "biothings_client" version))
       (sha256
        (base32 "0bccs37d5saxn5xsd2rfpkrnc5a120xs3ibizai66fgvp1vxbnc4"))))
    (build-system python-build-system)
    (arguments `(#:tests? #false)) ; require internet access
    (propagated-inputs (list python-requests))
    (home-page "https://github.com/biothings/biothings_client.py")
    (synopsis "Python client for BioThings API services")
    (description "This package provides a Python client for BioThings
API services.")
    (license license:bsd-3)))

(define-public python-mgatk
  (package
    (name "python-mgatk")
    (version "0.6.7")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/caleblareau/mgatk")
             ;; There is no tag for 0.6.7, but this is the commit
             ;; corresponding to the version bump.
             (commit "2633903acb1fb406bb58c787f320c3641f446ee7")))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          ;; The md5 module has been removed in Python 3
          (add-after 'unpack 'python3-compatibility
            (lambda _
              (substitute* "tests/test_cli.py"
                (("import md5") "from hashlib import md5")
                (("md5.new") "md5")
                (("\\.digest") ".hexdigest")))))))
    (propagated-inputs
     (list python-biopython
           python-click
           python-numpy
           python-optparse-pretty
           python-pandas
           python-pysam
           python-regex
           python-ruamel.yaml
           snakemake))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/caleblareau/mgatk")
    (synopsis "Mitochondrial genome analysis toolkit.")
    (description "This package is a Python-based command line interface for
processing .bam files with mitochondrial reads and generating high-quality
heteroplasmy estimation from sequencing data.  The mgatk package places a
special emphasis on mitochondrial genotypes generated from single-cell
genomics data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell
ATAC-sequence}, but is generally applicable across other assays.")
    (license license:expat)))

(define-public python-multivelo
  (package
    (name "python-multivelo")
    (version "0.1.2")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "multivelo" version))
              (sha256
               (base32
                "1b4qyngwagh5sc2ygyfqyirg63myzh1g1glk03a1ykxfii32cjlp"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #f                       ;pypi source does not contain tests
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'sanity-check 'set-env
            (lambda _
              ;; numba RuntimeError: cannot cache function 'rdist'
              (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (native-inputs (list python-pypa-build))
    (propagated-inputs
     (list python-anndata
           python-h5py
           python-ipywidgets
           python-joblib
           python-loompy
           python-matplotlib
           python-numba
           python-numpy
           python-pandas
           python-scanpy
           python-scikit-learn
           python-scipy
           python-seaborn
           python-tqdm
           python-umap-learn
           scvelo))
    (home-page "https://github.com/welch-lab/MultiVelo")
    (synopsis "Velocity inference from single-cell multi-omic data")
    (description "MultiVelo uses a probabilistic latent variable model to
estimate the switch time and rate parameters of gene regulation, providing a
quantitative summary of the temporal relationship between epigenomic and
transcriptomic changes.")
    (license license:bsd-3)))

(define-public python-mygene
  (package
    (name "python-mygene")
    (version "3.2.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "mygene" version))
       (sha256
        (base32 "1snszwdgfygchxshcbry3b5pbcw3g1isp8dw46razxccqaxwlag7"))))
    (build-system python-build-system)
    (propagated-inputs
     (list python-biothings-client))
    (home-page "https://github.com/biothings/mygene.py")
    (synopsis "Python Client for MyGene.Info services")
    (description "MyGene.Info provides simple-to-use REST web services
to query/retrieve gene annotation data.  It's designed with simplicity
and performance emphasized.  Mygene is a Python wrapper to access
MyGene.Info services.")
    (license license:bsd-3)))

;; We cannot use the latest commit because it requires Java 9.
(define-public java-forester
  (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
        (revision "1"))
    (package
      (name "java-forester")
      (version (string-append "0-" revision "." (string-take commit 7)))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/cmzmasek/forester")
                      (commit commit)))
                (file-name (string-append name "-" version "-checkout"))
                (sha256
                 (base32
                  "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z"))
                (modules '((guix build utils)))
                (snippet
                 '(begin
                    ;; Delete bundled jars and pre-built classes
                    (delete-file-recursively "forester/java/resources")
                    (delete-file-recursively "forester/java/classes")
                    (for-each delete-file (find-files "forester/java/" "\\.jar$"))
                    ;; Delete bundled applications
                    (delete-file-recursively "forester_applications")
                    #t))))
      (build-system ant-build-system)
      (arguments
       `(#:tests? #f ; there are none
         #:jdk ,icedtea-8
         #:modules ((guix build ant-build-system)
                    (guix build utils)
                    (guix build java-utils)
                    (sxml simple)
                    (sxml transform))
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'chdir
             (lambda _ (chdir "forester/java") #t))
           (add-after 'chdir 'fix-dependencies
             (lambda _
               (chmod "build.xml" #o664)
               (call-with-output-file "build.xml.new"
                 (lambda (port)
                   (sxml->xml
                    (pre-post-order
                     (with-input-from-file "build.xml"
                       (lambda _ (xml->sxml #:trim-whitespace? #t)))
                     `(;; Remove all unjar tags to avoid repacking classes.
                       (unjar     . ,(lambda _ '()))
                       (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
                       (*text*    . ,(lambda (_ txt) txt))))
                    port)))
               (rename-file "build.xml.new" "build.xml")
               #t))
           ;; FIXME: itext is difficult to package as it depends on a few
           ;; unpackaged libraries.
           (add-after 'chdir 'remove-dependency-on-unpackaged-itext
             (lambda _
               (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
               (substitute* "src/org/forester/archaeopteryx/MainFrame.java"
                 (("pdf_written_to = PdfExporter.*")
                  "throw new IOException(\"PDF export is not available.\");"))
               #t))
           ;; There is no install target
           (replace 'install (install-jars ".")))))
      (propagated-inputs
       (list java-commons-codec java-openchart2))
      (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
      (synopsis "Phylogenomics libraries for Java")
      (description "Forester is a collection of Java libraries for
phylogenomics and evolutionary biology research.  It includes support for
reading, writing, and exporting phylogenetic trees.")
      (license license:lgpl2.1+))))

(define-public java-forester-1.005
  (package
    (name "java-forester")
    (version "1.005")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://repo1.maven.org/maven2/"
                                  "org/biojava/thirdparty/forester/"
                                  version "/forester-" version "-sources.jar"))
              (file-name (string-append name "-" version ".jar"))
              (sha256
               (base32
                "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv"))))
    (build-system ant-build-system)
    (arguments
     `(#:tests? #f ; there are none
       #:jdk ,icedtea-8
       #:modules ((guix build ant-build-system)
                  (guix build utils)
                  (guix build java-utils)
                  (sxml simple)
                  (sxml transform))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-dependencies
           (lambda* (#:key inputs #:allow-other-keys)
             (call-with-output-file "build.xml"
               (lambda (port)
                 (sxml->xml
                  (pre-post-order
                   (with-input-from-file "src/build.xml"
                     (lambda _ (xml->sxml #:trim-whitespace? #t)))
                   `(;; Remove all unjar tags to avoid repacking classes.
                     (unjar     . ,(lambda _ '()))
                     (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
                     (*text*    . ,(lambda (_ txt) txt))))
                  port)))
             (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml")
                        "synth_look_and_feel_1.xml")
             (copy-file (assoc-ref inputs "phyloxml.xsd")
                        "phyloxml.xsd")
             (substitute* "build.xml"
               (("../resources/synth_laf/synth_look_and_feel_1.xml")
                "synth_look_and_feel_1.xml")
               (("../resources/phyloxml_schema/1.10/phyloxml.xsd")
                "phyloxml.xsd"))
             #t))
         ;; FIXME: itext is difficult to package as it depends on a few
         ;; unpackaged libraries.
         (add-after 'unpack 'remove-dependency-on-unpackaged-itext
           (lambda _
             (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
             (substitute* '("src/org/forester/archaeopteryx/MainFrame.java"
                            "src/org/forester/archaeopteryx/MainFrameApplication.java")
               (("pdf_written_to = PdfExporter.*")
                "throw new IOException(\"PDF export is not available.\"); /*")
               ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/")
               (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/"))
             #t))
         (add-after 'unpack 'delete-pre-built-classes
           (lambda _ (delete-file-recursively "src/classes") #t))
         ;; There is no install target
         (replace 'install (install-jars ".")))))
    (propagated-inputs
     (list java-commons-codec java-openchart2))
    ;; The source archive does not contain the resources.
    (native-inputs
     `(("phyloxml.xsd"
        ,(origin
           (method url-fetch)
           (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
                               "b61cc2dcede0bede317db362472333115756b8c6/"
                               "forester/resources/phyloxml_schema/1.10/phyloxml.xsd"))
           (file-name (string-append name "-phyloxml-" version ".xsd"))
           (sha256
            (base32
             "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv"))))
       ("synth_look_and_feel_1.xml"
        ,(origin
           (method url-fetch)
           (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
                               "29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
                               "forester/java/classes/resources/"
                               "synth_look_and_feel_1.xml"))
           (file-name (string-append name "-synth-look-and-feel-" version ".xml"))
           (sha256
            (base32
             "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h"))))))
    (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
    (synopsis "Phylogenomics libraries for Java")
    (description "Forester is a collection of Java libraries for
phylogenomics and evolutionary biology research.  It includes support for
reading, writing, and exporting phylogenetic trees.")
    (license license:lgpl2.1+)))

(define-public java-biojava-core
  (package
    (name "java-biojava-core")
    (version "4.2.11")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biojava/biojava")
                    (commit (string-append "biojava-" version))))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk"))))
    (build-system ant-build-system)
    (arguments
     `(#:jdk ,icedtea-8
       #:jar-name "biojava-core.jar"
       #:source-dir "biojava-core/src/main/java/"
       #:test-dir "biojava-core/src/test"
       ;; These tests seem to require internet access.
       #:test-exclude (list "**/SearchIOTest.java"
                            "**/BlastXMLParserTest.java"
                            "**/GenbankCookbookTest.java"
                            "**/GenbankProxySequenceReaderTest.java")
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'copy-resources
           (lambda _
             (copy-recursively "biojava-core/src/main/resources"
                               "build/classes")
             #t))
         (add-before 'check 'copy-test-resources
           (lambda _
             (copy-recursively "biojava-core/src/test/resources"
                               "build/test-classes")
             #t)))))
    (propagated-inputs
     (list java-log4j-api java-log4j-core java-slf4j-api
           java-slf4j-simple))
    (native-inputs
     (list java-junit java-hamcrest-core))
    (home-page "https://biojava.org")
    (synopsis "Core libraries of Java framework for processing biological data")
    (description "BioJava is a project dedicated to providing a Java framework
for processing biological data.  It provides analytical and statistical
routines, parsers for common file formats, reference implementations of
popular algorithms, and allows the manipulation of sequences and 3D
structures.  The goal of the biojava project is to facilitate rapid
application development for bioinformatics.

This package provides the core libraries.")
    (license license:lgpl2.1+)))

(define-public java-biojava-phylo
  (package (inherit java-biojava-core)
    (name "java-biojava-phylo")
    (build-system ant-build-system)
    (arguments
     `(#:jdk ,icedtea-8
       #:jar-name "biojava-phylo.jar"
       #:source-dir "biojava-phylo/src/main/java/"
       #:test-dir "biojava-phylo/src/test"
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'copy-resources
           (lambda _
             (copy-recursively "biojava-phylo/src/main/resources"
                               "build/classes")
             #t))
         (add-before 'check 'copy-test-resources
           (lambda _
             (copy-recursively "biojava-phylo/src/test/resources"
                               "build/test-classes")
             #t)))))
    (propagated-inputs
     (list java-log4j-api
           java-log4j-core
           java-slf4j-api
           java-slf4j-simple
           java-biojava-core
           java-forester))
    (native-inputs
     (list java-junit java-hamcrest-core))
    (home-page "https://biojava.org")
    (synopsis "Biojava interface to the forester phylogenomics library")
    (description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))

(define-public java-biojava-alignment
  (package (inherit java-biojava-core)
    (name "java-biojava-alignment")
    (build-system ant-build-system)
    (arguments
     `(#:jdk ,icedtea-8
       #:jar-name "biojava-alignment.jar"
       #:source-dir "biojava-alignment/src/main/java/"
       #:test-dir "biojava-alignment/src/test"
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'copy-resources
           (lambda _
             (copy-recursively "biojava-alignment/src/main/resources"
                               "build/classes")
             #t))
         (add-before 'check 'copy-test-resources
           (lambda _
             (copy-recursively "biojava-alignment/src/test/resources"
                               "build/test-classes")
             #t)))))
    (propagated-inputs
     (list java-log4j-api
           java-log4j-core
           java-slf4j-api
           java-slf4j-simple
           java-biojava-core
           java-biojava-phylo
           java-forester))
    (native-inputs
     (list java-junit java-hamcrest-core))
    (home-page "https://biojava.org")
    (synopsis "Biojava API for genetic sequence alignment")
    (description "The alignment module of BioJava provides an API that
contains

@itemize
@item implementations of dynamic programming algorithms for sequence
  alignment;
@item reading and writing of popular alignment file formats;
@item a single-, or multi- threaded multiple sequence alignment algorithm.
@end itemize\n")))

(define-public java-biojava-core-4.0
  (package (inherit java-biojava-core)
    (name "java-biojava-core")
    (version "4.0.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biojava/biojava")
                    (commit (string-append "biojava-" version))))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8"))))))

(define-public java-biojava-phylo-4.0
  (package (inherit java-biojava-core-4.0)
    (name "java-biojava-phylo")
    (build-system ant-build-system)
    (arguments
     `(#:jdk ,icedtea-8
       #:jar-name "biojava-phylo.jar"
       #:source-dir "biojava-phylo/src/main/java/"
       #:test-dir "biojava-phylo/src/test"
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'copy-resources
           (lambda _
             (copy-recursively "biojava-phylo/src/main/resources"
                               "build/classes")
             #t))
         (add-before 'check 'copy-test-resources
           (lambda _
             (copy-recursively "biojava-phylo/src/test/resources"
                               "build/test-classes")
             #t)))))
    (propagated-inputs
     (list java-log4j-api
           java-log4j-core
           java-slf4j-api
           java-slf4j-simple
           java-biojava-core-4.0
           java-forester-1.005))
    (native-inputs
     (list java-junit java-hamcrest-core))
    (home-page "https://biojava.org")
    (synopsis "Biojava interface to the forester phylogenomics library")
    (description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))

(define-public java-biojava-alignment-4.0
  (package (inherit java-biojava-core-4.0)
    (name "java-biojava-alignment")
    (build-system ant-build-system)
    (arguments
     `(#:jdk ,icedtea-8
       #:jar-name "biojava-alignment.jar"
       #:source-dir "biojava-alignment/src/main/java/"
       #:test-dir "biojava-alignment/src/test"
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'copy-resources
           (lambda _
             (copy-recursively "biojava-alignment/src/main/resources"
                               "build/classes")
             #t))
         (add-before 'check 'copy-test-resources
           (lambda _
             (copy-recursively "biojava-alignment/src/test/resources"
                               "build/test-classes")
             #t)))))
    (propagated-inputs
     (list java-log4j-api
           java-log4j-core
           java-slf4j-api
           java-slf4j-simple
           java-biojava-core-4.0
           java-biojava-phylo-4.0
           java-forester-1.005))
    (native-inputs
     (list java-junit java-hamcrest-core))
    (home-page "https://biojava.org")
    (synopsis "Biojava API for genetic sequence alignment")
    (description "The alignment module of BioJava provides an API that
contains

@itemize
@item implementations of dynamic programming algorithms for sequence
  alignment;
@item reading and writing of popular alignment file formats;
@item a single-, or multi- threaded multiple sequence alignment algorithm.
@end itemize\n")))

(define-public dropseq-tools
  (package
    (name "dropseq-tools")
    (version "1.13")
    (source
     (origin
       (method url-fetch)
       (uri "http://mccarrolllab.com/download/1276/")
       (file-name (string-append "dropseq-tools-" version ".zip"))
       (sha256
        (base32
         "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
       ;; Delete bundled libraries
       (modules '((guix build utils)))
       (snippet
        '(begin
           (for-each delete-file (find-files "jar/lib" "\\.jar$"))
           (delete-file-recursively "3rdParty")))))
    (build-system ant-build-system)
    (arguments
     `(#:tests? #f                      ; test data are not included
       #:test-target "test"
       #:build-target "all"
       #:source-dir "public/src/"
       #:jdk ,icedtea-8
       #:make-flags
       (list ,#~(string-append "-Dpicard.executable.dir="
                               #$(this-package-input "java-picard")
                               "/share/java/"))
       #:modules ((ice-9 match)
                  (srfi srfi-1)
                  (guix build utils)
                  (guix build java-utils)
                  (guix build ant-build-system))
       #:phases
       (modify-phases %standard-phases
         ;; FIXME: fails with "java.io.FileNotFoundException:
         ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar"
         (delete 'generate-jar-indices)
         ;; All dependencies must be linked to "lib", because that's where
         ;; they will be searched for when the Class-Path property of the
         ;; manifest is computed.
         (add-after 'unpack 'record-references
	   (lambda* (#:key inputs #:allow-other-keys)
             (mkdir-p "jar/lib")
             (let ((dirs (filter-map (match-lambda
                                       ((name . dir)
                                        (if (and (string-prefix? "java-" name)
                                                 (not (string=? name "java-testng")))
                                            dir #f)))
                                     inputs)))
               (for-each (lambda (jar)
                           (symlink jar (string-append "jar/lib/" (basename jar))))
                         (append-map (lambda (dir) (find-files dir "\\.jar$"))
                                     dirs)))))
         ;; There is no installation target
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out     (assoc-ref outputs "out"))
                    (bin     (string-append out "/bin"))
                    (share   (string-append out "/share/java/"))
                    (lib     (string-append share "/lib/"))
                    (scripts (list "BAMTagHistogram"
                                   "BAMTagofTagCounts"
                                   "BaseDistributionAtReadPosition"
                                   "CollapseBarcodesInPlace"
                                   "CollapseTagWithContext"
                                   "ConvertToRefFlat"
                                   "CreateIntervalsFiles"
                                   "DetectBeadSynthesisErrors"
                                   "DigitalExpression"
                                   "Drop-seq_alignment.sh"
                                   "FilterBAM"
                                   "FilterBAMByTag"
                                   "GatherGeneGCLength"
                                   "GatherMolecularBarcodeDistributionByGene"
                                   "GatherReadQualityMetrics"
                                   "PolyATrimmer"
                                   "ReduceGTF"
                                   "SelectCellsByNumTranscripts"
                                   "SingleCellRnaSeqMetricsCollector"
                                   "TagBamWithReadSequenceExtended"
                                   "TagReadWithGeneExon"
                                   "TagReadWithInterval"
                                   "TrimStartingSequence"
                                   "ValidateReference")))
               (for-each mkdir-p (list bin share lib))
               (install-file "dist/dropseq.jar" share)
               (for-each (lambda (script)
                           (chmod script #o555)
                           (install-file script bin))
                         scripts)
               (substitute* (map (lambda (script)
                                   (string-append bin "/" script))
                                 scripts)
                 (("^java") (which "java"))
                 (("jar_deploy_dir=.*")
                  (string-append "jar_deploy_dir=" share "\n"))))))
         ;; FIXME: We do this after stripping jars because we don't want it to
         ;; copy all these jars and strip them.  We only want to install
         ;; links.  Arguably, this is a problem with the ant-build-system.
         (add-after 'strip-jar-timestamps 'install-links
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out     (assoc-ref outputs "out"))
                    (share   (string-append out "/share/java/"))
                    (lib     (string-append share "/lib/")))
               (for-each (lambda (jar)
                           (symlink (readlink jar)
                                    (string-append lib (basename jar))))
                         (find-files "jar/lib" "\\.jar$"))))))))
    (inputs
     `(("jdk" ,icedtea-8)
       ("java-picard" ,java-picard-2.10.3)
       ("java-log4j-1.2-api" ,java-log4j-1.2-api)
       ("java-commons-math3" ,java-commons-math3)
       ("java-commons-jexl2" ,java-commons-jexl-2)
       ("java-commons-collections4" ,java-commons-collections4)
       ("java-commons-lang2" ,java-commons-lang)
       ("java-commons-io" ,java-commons-io)
       ("java-snappy-1.0.3-rc3" ,java-snappy-1)
       ("java-guava" ,java-guava)
       ("java-la4j" ,java-la4j)
       ("java-biojava-core" ,java-biojava-core-4.0)
       ("java-biojava-alignment" ,java-biojava-alignment-4.0)
       ("java-jdistlib" ,java-jdistlib)
       ("java-simple-xml" ,java-simple-xml)
       ("java-snakeyaml" ,java-snakeyaml)))
    (native-inputs
     (list unzip java-testng))
    (home-page "http://mccarrolllab.com/dropseq/")
    (synopsis "Tools for Drop-seq analyses")
    (description "Drop-seq is a technology to enable biologists to
analyze RNA expression genome-wide in thousands of individual cells at
once.  This package provides tools to perform Drop-seq analyses.")
    (license license:expat)))

(define-public pigx-rnaseq
  (package
    (name "pigx-rnaseq")
    (version "0.1.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
                                  "releases/download/v" version
                                  "/pigx_rnaseq-" version ".tar.gz"))
              (sha256
               (base32
                "0mlas0srl04mvgsyydm67gg5syijf1k2f6dy7bdqqxc70fywfd08"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-tests? #f             ; not supported
       #:phases
       (modify-phases %standard-phases
         ;; "test.sh" runs the whole pipeline, which takes a long time and
         ;; might fail due to OOM.  The MultiQC is also resource intensive.
         (add-after 'unpack 'disable-resource-intensive-test
           (lambda _
             (substitute* "Makefile.in"
               (("^  tests/test_multiqc/test.sh") "")
               (("^  test.sh") ""))))
         (add-before 'bootstrap 'autoreconf
           (lambda _
             (invoke "autoreconf" "-vif")))
         (add-before 'configure 'set-PYTHONPATH
           (lambda _
             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
         (add-before 'check 'set-timezone
           ;; The readr package is picky about timezones.
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "TZ" "UTC+1")
             (setenv "TZDIR"
                     (search-input-directory inputs
                                             "share/zoneinfo")))))))
    (inputs
     (list coreutils
           sed
           gzip
           snakemake
           megadepth
           multiqc
           star-for-pigx
           hisat2
           fastp
           htseq
           samtools
           r-minimal
           r-rmarkdown
           r-ggplot2
           r-ggpubr
           r-ggrepel
           r-gprofiler2
           r-deseq2
           r-dt
           r-knitr
           r-pheatmap
           r-corrplot
           r-reshape2
           r-plotly
           r-scales
           r-summarizedexperiment
           r-crosstalk
           r-tximport
           r-rtracklayer
           r-rjson
           salmon
           pandoc
           python-wrapper
           python-deeptools
           python-pyyaml))
    (native-inputs
     (list tzdata automake autoconf))
    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
    (synopsis "Analysis pipeline for RNA sequencing experiments")
    (description "PiGX RNAseq is an analysis pipeline for preprocessing and
reporting for RNA sequencing experiments.  It is easy to use and produces high
quality reports.  The inputs are reads files from the sequencing experiment,
and a configuration file which describes the experiment.  In addition to
quality control of the experiment, the pipeline produces a differential
expression report comparing samples in an easily configurable manner.")
    (license license:gpl3+)))

(define-public pigx-chipseq
  (package
    (name "pigx-chipseq")
    (version "0.1.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
                                  "releases/download/v" version
                                  "/pigx_chipseq-" version ".tar.gz"))
              (sha256
               (base32
                "008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; parts of the tests rely on access to the network
       #:phases
       (modify-phases %standard-phases
         (add-before 'configure 'set-PYTHONPATH
           (lambda _
             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
    (inputs
     (list grep
           coreutils
           r-minimal
           r-argparser
           r-biocparallel
           r-biostrings
           r-chipseq
           r-corrplot
           r-data-table
           r-deseq2
           r-dplyr
           r-dt
           r-genomation
           r-genomicalignments
           r-genomicranges
           r-ggplot2
           r-ggrepel
           r-gprofiler2
           r-heatmaply
           r-hexbin
           r-htmlwidgets
           r-jsonlite
           r-pheatmap
           r-plotly
           r-rmarkdown
           r-rsamtools
           r-rsubread
           r-rtracklayer
           r-s4vectors
           r-stringr
           r-tibble
           r-tidyr
           python-wrapper
           python-pyyaml
           python-magic
           python-xlrd
           trim-galore
           macs
           multiqc
           perl
           pandoc
           fastqc
           bowtie
           idr
           snakemake
           samtools
           bedtools
           kentutils))
    (native-inputs
     (list python-pytest))
    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
    (synopsis "Analysis pipeline for ChIP sequencing experiments")
    (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
calling and reporting for ChIP sequencing experiments.  It is easy to use and
produces high quality reports.  The inputs are reads files from the sequencing
experiment, and a configuration file which describes the experiment.  In
addition to quality control of the experiment, the pipeline enables to set up
multiple peak calling analysis and allows the generation of a UCSC track hub
in an easily configurable manner.")
    (license license:gpl3+)))

(define-public pigx-bsseq
  (package
    (name "pigx-bsseq")
    (version "0.1.8")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
                                  "releases/download/v" version
                                  "/pigx_bsseq-" version ".tar.gz"))
              (sha256
               (base32
                "1s8zgrqxabrawrgkga5rmgb0gyzj7ck47p3rkicjkfv7r2yjy0d7"))))
    (build-system gnu-build-system)
    (arguments
     `(;; TODO: tests currently require 12+GB of RAM.  See
       ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
       #:tests? #f
       #:phases
       (modify-phases %standard-phases
         (add-before 'configure 'set-PYTHONPATH
           (lambda _
             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
         (add-before 'check 'set-timezone
           ;; The readr package is picky about timezones.
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "TZ" "UTC+1")
             (setenv "TZDIR"
                     (search-input-directory inputs
                                             "share/zoneinfo")))))))
    (native-inputs
     (list tzdata))
    (inputs
     (list coreutils
           sed
           grep
           r-minimal
           r-annotationhub
           r-dt
           r-genomation
           r-ggbio
           r-ggrepel
           r-matrixstats
           r-methylkit
           r-reshape2
           r-rtracklayer
           r-rmarkdown
           r-bookdown
           r-ggplot2
           r-ggbio
           pandoc
           python-wrapper
           python-pyyaml
           snakemake
           bismark
           bowtie
           bwa-meth
           fastqc
           methyldackel
           multiqc
           trim-galore
           cutadapt
           samblaster
           samtools))
    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
    (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
    (description "PiGx BSseq is a data processing pipeline for raw fastq read
data of bisulfite experiments; it produces reports on aggregate methylation
and coverage and can be used to produce information on differential
methylation and segmentation.")
    (license license:gpl3+)))

(define-public pigx-scrnaseq
  (package
    (name "pigx-scrnaseq")
    (version "1.1.9")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
                                  "releases/download/v" version
                                  "/pigx_scrnaseq-" version ".tar.gz"))
              (sha256
               (base32
                "0adx7877c3lhlrzfid76i8bc829wcmzvrm0jx47gyid8mxqb7vqs"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'configure 'set-additional-environment-variables
           (lambda _
             ;; Needed because of loompy
             (setenv "NUMBA_CACHE_DIR" "/tmp")
             ;; Needed to capture environment
             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
    (inputs
     (list coreutils
           perl
           fastqc
           flexbar
           icedtea-8
           jellyfish
           python-wrapper
           python-pyyaml
           python-pandas
           python-magic
           python-numpy
           python-loompy
           pandoc
           samtools
           snakemake
           star-for-pigx
           r-minimal
           r-argparser
           r-cowplot
           r-data-table
           r-delayedarray
           r-delayedmatrixstats
           r-dplyr
           r-dropbead
           r-dt
           r-genomicalignments
           r-genomicfiles
           r-genomicranges
           r-ggplot2
           r-hdf5array
           r-pheatmap
           r-rmarkdown
           r-rsamtools
           r-rtracklayer
           r-rtsne
           r-scater
           r-scran
           r-seurat
           r-singlecellexperiment
           r-stringr
           r-yaml))
    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
    (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
    (description
     "PiGX scRNAseq is an analysis pipeline for preprocessing and
quality control for single cell RNA sequencing experiments.  The inputs are
read files from the sequencing experiment, and a configuration file which
describes the experiment.  It produces processed files for downstream analysis
and interactive quality reports.  The pipeline is designed to work with UMI
based methods.")
    (license license:gpl3+)))

(define-public pigx-sars-cov-2
  (package
    (name "pigx-sars-cov-2")
    (version "0.0.9")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sars-cov-2"
                                  "/releases/download/v" version
                                  "/pigx_sars-cov-2-" version ".tar.gz"))
              (sha256
               (base32
                "168hrafgsn165q3hcdn916vlbl0zbzri1lckaqapbrcqk00izxma"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'unpack-databases
           (lambda* (#:key inputs #:allow-other-keys)
             ;; The tests need to be able to write caches to HOME.
             ;; They also default to reading the databases from there.
             (setenv "HOME" "/tmp")
             ;; Unpack the three databases in the expected location.
             (let ((root "/tmp/.local/share/pigx/databases")
                   (use-underscore (lambda (c) (if (equal? c #\-) #\_ c))))
               (for-each (lambda (db)
                           (let ((where (string-append root "/"
                                                       (string-map use-underscore db))))
                             (mkdir-p where)
                             (invoke "tar" "-C" where
                                     "-xf" (assoc-ref inputs db))))
                         '("kraken-db" "krona-db" "vep-db")))))
         (add-before 'configure 'set-PYTHONPATH
           (lambda _
             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
    (native-inputs
     (let ((bimsb-origin
            (lambda (name hash)
              (origin
                (method url-fetch)
                (uri
                 (string-append "https://bimsbstatic.mdc-berlin.de/akalin/AAkalin_pathogenomics"
                                "/databases_small-20221006/" name))
                (sha256 (base32 hash))))))
       `(("kraken-db"
          ,(bimsb-origin
            "kraken_db.tar.gz"
            "0sdm4xh5npg6c3y2pz8xgphim4qpglm8wdid6rlaaqsn6iikv0mz"))
         ("krona-db"
          ,(bimsb-origin
            "krona_db.tar.gz"
            "1rwy4gd3vw1gdjldrgf44c1xaa3vq8i3pgisjhrac81yx63x8f2h"))
         ("vep-db"
          ,(bimsb-origin
            "vep_db.tar.gz"
            "0d8hhi43zsw3wqm7gd0z0gpcdsc6h6ra0imn87hifl9a64jxqzxz")))))
    (inputs
     (list bash-minimal
           bedtools
           bwa
           ensembl-vep
           fastp
           fastqc
           ivar
           kraken2
           krona-tools
           lofreq
           multiqc
           python-pyyaml
           python-wrapper
           r-base64url
           r-data-table
           r-deconvr
           r-dplyr
           r-dt
           r-ggplot2
           r-htmltools
           r-jsonlite
           r-knitr
           r-magrittr
           r-mass
           r-minimal
           r-plotly
           r-qpcr
           r-r-utils
           r-reshape2
           r-rmarkdown
           r-stringr
           r-tidyr
           r-viridis
           samtools
           snakemake
           wget))
    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
    (synopsis "Analysis pipeline for wastewater sequencing")
    (description "PiGx SARS-CoV-2 is a pipeline for analysing data from
sequenced wastewater samples and identifying given variants-of-concern of
SARS-CoV-2.  The pipeline can be used for continuous sampling.  The output
report will provide an intuitive visual overview about the development of
variant abundance over time and location.")
    (license license:gpl3+)))

(define-public pigx-sars-cov2-ww
  (deprecated-package "pigx-sars-cov2-ww" pigx-sars-cov-2))

(define-public pigx
  (package
    (name "pigx")
    (version "0.0.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
                                  "releases/download/v" version
                                  "/pigx-" version ".tar.gz"))
              (sha256
               (base32
                "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7"))))
    (build-system gnu-build-system)
    (inputs
     (list python pigx-bsseq pigx-chipseq pigx-rnaseq pigx-scrnaseq))
    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
    (synopsis "Analysis pipelines for genomics")
    (description "PiGx is a collection of genomics pipelines.  It includes the
following pipelines:

@itemize
@item PiGx BSseq for raw fastq read data of bisulfite experiments
@item PiGx RNAseq for RNAseq samples
@item PiGx scRNAseq for single cell dropseq analysis
@item PiGx ChIPseq for reads from ChIPseq experiments
@end itemize

All pipelines are easily configured with a simple sample sheet and a
descriptive settings file.  The result is a set of comprehensive, interactive
HTML reports with interesting findings about your samples.")
    (license license:gpl3+)))

(define-public genrich
  (package
    (name "genrich")
    (version "0.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/jsh58/Genrich")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0x0q6z0208n3cxzqjla4rgjqpyqgwpmz27852lcvzkzaigymq4zp"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; there are none
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin"))
             #t)))))
    (inputs
     (list zlib))
    (home-page "https://github.com/jsh58/Genrich")
    (synopsis "Detecting sites of genomic enrichment")
    (description "Genrich is a peak-caller for genomic enrichment
assays (e.g. ChIP-seq, ATAC-seq).  It analyzes alignment files generated
following the assay and produces a file detailing peaks of significant
enrichment.")
    (license license:expat)))

(define-public mantis
  ;; This is an arbitrary commit as a year has passed since 0.1 was tagged.
  (let ((commit "b6979a269172a45201c8366680d8b889f889432b")
        (revision "2"))
    (package
      (name "mantis")
      (version (git-version "0.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/splatlab/mantis")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0dq8a785hnaxx5kq757m5czs8xpcjpcph1inq2nm8h6zfvqyj8xs"))))
      (build-system cmake-build-system)
      (arguments
       '(#:tests? #f ; there are none
         #:configure-flags (list "-DNH=ON"))) ; do not use SSE4.2 instructions
      (inputs
       (list sdsl-lite openssl zlib))
      (native-inputs
       (list gcc-7))
      (home-page "https://github.com/splatlab/mantis")
      (synopsis "Large-scale sequence-search index data structure")
      (description "Mantis is a space-efficient data structure that can be
used to index thousands of raw-read genomics experiments and facilitate
large-scale sequence searches on those experiments.  Mantis uses counting
quotient filters instead of Bloom filters, enabling rapid index builds and
queries, small indexes, and exact results, i.e., no false positives or
negatives.  Furthermore, Mantis is also a colored de Bruijn graph
representation, so it supports fast graph traversal and other topological
analyses in addition to large-scale sequence-level searches.")
      ;; uses __uint128_t and inline assembly
      (supported-systems '("x86_64-linux"))
      (license license:bsd-3))))

(define-public sjcount
  ;; There is no tag for version 3.2, nor is there a release archive.
  (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
        (revision "1"))
    (package
      (name "sjcount")
      (version (git-version "3.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/pervouchine/sjcount-full")
                      (commit commit)))
                (file-name (string-append name "-" version "-checkout"))
                (sha256
                 (base32
                  "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f                    ; requires a 1.4G test file
         #:make-flags
         ,#~(list (string-append "SAMTOOLS_DIR="
                                 #$(this-package-input "samtools")
                                 "/lib/"))
         #:phases
         (modify-phases %standard-phases
           (replace 'configure
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* "makefile"
                 (("-I \\$\\{SAMTOOLS_DIR\\}")
                  (string-append "-I" (assoc-ref inputs "samtools")
                                 "/include/samtools"))
                 (("-lz ") "-lz -lpthread "))))
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (for-each (lambda (tool)
                           (install-file tool
                                         (string-append (assoc-ref outputs "out")
                                                        "/bin")))
                         '("j_count" "b_count" "sjcount")))))))
      (inputs
       (list samtools-0.1 zlib))
      (home-page "https://github.com/pervouchine/sjcount-full/")
      (synopsis "Annotation-agnostic splice junction counting pipeline")
      (description "Sjcount is a utility for fast quantification of splice
junctions in RNA-seq data.  It is annotation-agnostic and offset-aware.  This
version does count multisplits.")
      (license license:gpl3+))))

(define-public minimap2
  (package
    (name "minimap2")
    (version "2.28")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/lh3/minimap2/"
                           "releases/download/v" version "/"
                           "minimap2-" version ".tar.bz2"))
       (sha256
        (base32
         "1d50j9fdmmaj7sdf4f49xddc235f7032lwh5ijgi2afj6lkp39gz"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; there are none
       #:modules ((guix build utils)
                  (guix build gnu-build-system)
                  (srfi srfi-26))
       #:make-flags
       (list (string-append "CC=" ,(cc-for-target))
             (let ((system ,(or (%current-target-system)
                                (%current-system))))
               (cond
                 ((or (string-prefix? "i586" system)
                      (string-prefix? "i686" system))
                  "sse2only=1")
                 ((string-prefix? "armhf" system)
                  "arm_neon=1")
                 ((string-prefix? "aarch64" system)
                  "aarch64=1")
                 (else "all"))))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (lib (string-append out "/lib"))
                    (inc (string-append out "/include"))
                    (man (string-append out "/share/man/man1")))
               (install-file "minimap2" bin)
               (install-file "libminimap2.a" lib)
               (install-file "minimap2.1" man)
               (map (cut install-file <> inc)
                    (find-files "." "\\.h$"))
               ;; Not this file.
               (delete-file (string-append inc "/emmintrin.h"))
               (mkdir-p (string-append lib "/pkgconfig"))
               (with-output-to-file (string-append lib "/pkgconfig/minimap2.pc")
                (lambda _
                  (format #t "prefix=~a~@
                          exec_prefix=${prefix}~@
                          libdir=${exec_prefix}/lib~@
                          includedir=${prefix}/include~@
                          ~@
                          Name: libminimap2~@
                          Version: ~a~@
                          Description: A versatile pairwise aligner for genomic and spliced nucleotide sequence~@
                          Libs: -L${libdir} -lminimap2~@
                          Cflags: -I${includedir}~%"
                          out ,version)))))))))
    (inputs
     (list zlib))
    (home-page "https://lh3.github.io/minimap2/")
    (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
    (description "Minimap2 is a versatile sequence alignment program that
aligns DNA or mRNA sequences against a large reference database.  Typical use
cases include:

@enumerate
@item mapping PacBio or Oxford Nanopore genomic reads to the human genome;
@item finding overlaps between long reads with error rate up to ~15%;
@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
  reads against a reference genome;
@item aligning Illumina single- or paired-end reads;
@item assembly-to-assembly alignment;
@item full-genome alignment between two closely related species with
  divergence below ~15%.
@end enumerate\n")
    (license license:expat)))

(define-public python-mappy
  (package
   (name "python-mappy")
   (version "2.24")
   (source (origin
            (method url-fetch)
            (uri (pypi-uri "mappy" version))
            (sha256
             (base32
              "1ycszza87p9qvx8mis9v1hry0ac465x1xcxbsn1k45qlxxrzp8im"))))
   (build-system python-build-system)
   (native-inputs
    (list python-cython))
   (inputs
    (list zlib))
   (home-page "https://github.com/lh3/minimap2")
   (synopsis "Python binding for minimap2")
   (description "This package provides a convenient interface to minimap2,
a fast and accurate C program to align genomic and transcribe nucleotide
sequences.")
   (license license:expat)))

(define-public miniasm
  (package
   (name "miniasm")
   (version "0.3")
   (source (origin
            (method git-fetch)
            (uri (git-reference
                   (url "https://github.com/lh3/miniasm")
                   (commit (string-append "v" version))))
            (file-name (git-file-name name version))
            (sha256
             (base32
              "04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs"))))
   (build-system gnu-build-system)
   (inputs
    (list zlib))
   (arguments
    `(#:tests? #f ; There are no tests.
      #:phases
      (modify-phases %standard-phases
        (delete 'configure)
        (replace 'install
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
              (install-file "miniasm" bin)
              (install-file "minidot" bin)
              #t))))))
   (home-page "https://github.com/lh3/miniasm")
   (synopsis "Ultrafast de novo assembly for long noisy reads")
   (description "Miniasm is a very fast OLC-based de novo assembler for noisy
long reads.  It takes all-vs-all read self-mappings (typically by minimap) as
input and outputs an assembly graph in the GFA format.  Different from
mainstream assemblers, miniasm does not have a consensus step.  It simply
concatenates pieces of read sequences to generate the final unitig sequences.
Thus the per-base error rate is similar to the raw input reads.")
   (license license:expat)))

(define-public bandage
  (package
    (name "bandage")
    (version "0.8.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/rrwick/Bandage")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1bbsn5f5x8wlspg4pbibqz6m5vin8c19nl224f3z3km0pkc97rwv"))))
    (build-system qt-build-system)
    (arguments
     (list
      ;; TODO: Once <https://issues.guix.gnu.org/47475> is fixed,
      ;; consider uncommenting the following:
      ;;
      ;; Prevent the (rarely updated) imagemagick/stable package from
      ;; ending up in the closure.
      ;; #:disallowed-references (list imagemagick/stable)
      #:phases
      #~(modify-phases %standard-phases
          (replace 'configure
            (lambda _
              (invoke "qmake" "Bandage.pro")))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (substitute* "tests/bandage_command_line_tests.sh"
                  (("^bandagepath=.*")
                   (string-append "bandagepath=" (getcwd) "/Bandage\n")))
                (with-directory-excursion "tests"
                  (setenv "XDG_RUNTIME_DIR" (getcwd))
                  (invoke "./bandage_command_line_tests.sh")))))
          (replace 'install
            (lambda _
              (install-file "Bandage" (string-append #$output "/bin")))))))
    (inputs
     (list qtbase-5 qtsvg-5))
    (native-inputs
     ;; imagemagick/stable cannot be used here, as it will end up in
     ;; the closure.  See <https://issues.guix.gnu.org/47475>.
     (list imagemagick))
    (home-page "https://rrwick.github.io/Bandage/")
    (synopsis
     "Bioinformatics Application for Navigating De novo Assembly Graphs Easily")
    (description "Bandage is a program for visualising de novo assembly graphs.
It allows users to interact with the assembly graphs made by de novo assemblers
such as Velvet, SPAdes, MEGAHIT and others.  De novo assembly graphs contain not
only assembled contigs but also the connections between those contigs, which
were previously not easily accessible.  Bandage visualises assembly graphs, with
connections, using graph layout algorithms.  Nodes in the drawn graph, which
represent contigs, can be automatically labelled with their ID, length or depth.
Users can interact with the graph by moving, labelling and colouring nodes.
Sequence information can also be extracted directly from the graph viewer.  By
displaying connections between contigs, Bandage opens up new possibilities for
analysing and improving de novo assemblies that are not possible by looking at
contigs alone.")
    (license (list license:gpl2+        ; bundled ogdf
                   license:gpl3+))))

(define-public libmaus2
  (package
    (name "libmaus2")
    (version "2.0.786")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://gitlab.com/german.tischler/libmaus2")
                    (commit (string-append version "-release-20210531143054"))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1rxakmwjcx2yq5sjh3v849f7dfw4xzc2fyzf6s28s3p95z84w564"))))
    (build-system gnu-build-system)
    ;; The test suite attempts to execute ../test-driver, which does not exist.
    (arguments '(#:tests? #false))
    (propagated-inputs
     (list zlib))
    (native-inputs
     (list pkg-config))
    (home-page "https://gitlab.com/german.tischler/libmaus2")
    (synopsis "Collection of data structures and algorithms useful for bioinformatics")
    (description "libmaus2 is a collection of data structures and
algorithms.  It contains:

@itemize
@item I/O classes (single byte and UTF-8);
@item @code{bitio} classes (input, output and various forms of bit level
  manipulation);
@item text indexing classes (suffix and LCP array, fulltext and minute (FM),
  etc.);
@item BAM sequence alignment files input/output (simple and collating);
and many lower level support classes.
@end itemize\n")
    ;; The code is explicitly available under the terms of either GPLv2 or
    ;; GPLv3 according to the AUTHORS file, though most files have a GPLv3+
    ;; license header.
    (license (list license:gpl2+ license:gpl3+))))

(define-public biobambam2
  (package
    (name "biobambam2")
    (version "2.0.182")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://gitlab.com/german.tischler/biobambam2")
                    (commit (string-append version "-release-20210412001032"))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0b7w7a2a7hpkgrdn0n7hy4pilzrj82zqrh7q4bg1l0cd6bqr60m5"))))
    (build-system gnu-build-system)
    (arguments
     ;; The test suite attempts to execute ../test-driver, which does not exist.
     `(#:tests? #false
       #:configure-flags
       ,#~(list (string-append "--with-libmaus2="
                               #$(this-package-input "libmaus2")))))
    (inputs
     (list libmaus2 xerces-c))
    (native-inputs
     (list pkg-config))
    (home-page "https://gitlab.com/german.tischler/biobambam2")
    (synopsis "Tools for processing BAM files")
    (description "This package contains some tools for processing BAM files
including:

@itemize
@item bamsormadup: parallel sorting and duplicate marking
@item bamcollate2: reads BAM and writes BAM reordered such that alignment or
  collated by query name
@item bammarkduplicates: reads BAM and writes BAM with duplicate alignments
  marked using the BAM flags field
@item bammaskflags: reads BAM and writes BAM while masking (removing) bits
  from the flags column
@item bamrecompress: reads BAM and writes BAM with a defined compression
  setting.  This tool is capable of multi-threading.
@item bamsort: reads BAM and writes BAM resorted by coordinates or query name
@item bamtofastq: reads BAM and writes FastQ; output can be collated or
  uncollated by query name.
@end itemize
")
    ;; The COPYING file states that the code is distributed under version 3 of
    ;; the GPL, but the license headers include the "or later" clause.
    (license license:gpl3+)))

(define-public r-disgenet2r
  (let ((commit "8d8ce37da7384004038b25e784b9f7cfe2353de1")
        (revision "1"))
    (package
      (name "r-disgenet2r")
      (version (git-version "0.99.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://bitbucket.org/ibi_group/disgenet2r")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0dvk75s6wqssdyfn5iczldb8krvrz2s0dslxns4571cb2pr09b84"))))
      (properties `((upstream-name . "disgenet2r")))
      (build-system r-build-system)
      (propagated-inputs (list r-data-table
                               r-ggplot2
                               r-gtable
                               r-httr
                               r-igraph
                               r-jsonlite
                               r-purrr
                               r-reshape
                               r-reshape2
                               r-sparql
                               r-stringr
                               r-tidyr
                               r-tidyverse
                               r-venndiagram))
      (native-inputs (list r-knitr))
      (home-page "https://bitbucket.org/ibi_group/disgenet2r")
      (synopsis "Query, visualize, and expand DisGeNET data")
      (description
       "This is an R package to query and expand DisGeNET data, and to
visualize the results within R framework.  The disgenet2r package is designed
to retrieve data from DisGeNET v6.0 (Jan, 2019).")
      (license license:expat))))

(define-public r-dtmm
  (let ((commit "3a553b1e17d27d90a496d2e23e98e5dfe4abc266")
        (revision "1"))
    (package
      (name "r-dtmm")
      (version (git-version "0.1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/MaStatLab/DTMM")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "19279wafqfs9gk9489f8zsp52qcdb0mkxgvqszq4i733ckr2mmkk"))))
      (properties `((upstream-name . "DTMM")))
      (build-system r-build-system)
      (propagated-inputs (list r-ape r-rcpp r-rcpparmadillo))
      (home-page "https://github.com/MaStatLab/DTMM")
      (synopsis "Dirichlet-tree multinomial mixtures")
      (description
       "This package lets you perform unsupervised clustering of amplicon
sequencing data in microbiome studies with the Dirichlet-tree Multinomial
Mixtures.")
      (license license:cc0))))

;; Needed for r-liana
(define-public r-omnipathr/devel
  (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a")
        (revision "1"))
    (package
      (name "r-omnipathr")
      (version (git-version "3.5.5" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/saezlab/omnipathr")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq"))))
      (properties `((upstream-name . "OmnipathR")))
      (build-system r-build-system)
      (arguments
       `(#:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'set-HOME
             (lambda _ (setenv "HOME" "/tmp"))))))
      (propagated-inputs
       (list r-checkmate
             r-crayon
             r-curl
             r-digest
             r-dplyr
             r-httr
             r-igraph
             r-jsonlite
             r-later
             r-logger
             r-magrittr
             r-progress
             r-purrr
             r-rappdirs
             r-readr
             r-readxl
             r-rlang
             r-rvest
             r-stringr
             r-tibble
             r-tidyr
             r-tidyselect
             r-withr
             r-xml2
             r-yaml))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/saezlab/omnipathr")
      (synopsis "OmniPath web service client and more")
      (description
       "This package provides a client for the OmniPath web service and many
other resources.  It also includes functions to transform and pretty print
some of the downloaded data, functions to access a number of other resources
such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to
Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology,
InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015,
RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011.  Furthermore,
OmnipathR features a close integration with the NicheNet method for ligand
activity prediction from transcriptomics data, and its R implementation
@code{nichenetr}.")
      (license license:expat))))

(define-public r-liana
  (let ((commit "10d81773e0874de676eb106ce56e3cf9d4fe01d3")
        (revision "1"))
    (package
      (name "r-liana")
      (version (git-version "0.1.11" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/saezlab/liana/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0b0m8i9kava36s3cn6vnn5vmiwvqwxmcq8jacy6ccshsji3kgp09"))))
      (properties `((upstream-name . "liana")))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
           (add-after 'unpack 'set-HOME
             (lambda _ (setenv "HOME" "/tmp"))))))
      (propagated-inputs
       (list r-basilisk
             r-basilisk-utils
             r-complexheatmap
             r-dplyr
             r-ggplot2
             r-magrittr
             r-omnipathr/devel
             r-purrr
             r-rcolorbrewer
             r-readr
             r-reticulate
             r-rlang
             r-scater
             r-scran
             r-scuttle
             r-seuratobject
             r-singlecellexperiment
             r-stringr
             r-tibble
             r-tidyr
             r-tidyselect))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/saezlab/liana/")
      (synopsis "LIANA: a LIgand-receptor ANalysis frAmework")
      (description
       "LIANA provides a number of methods and resource for ligand-receptor
interaction inference from scRNA-seq data.")
      (license license:gpl3))))

(define-public r-circus
  (package
    (name "r-circus")
    (version "0.1.7")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BIMSBbioinfo/ciRcus")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0d1jz7r81zbcy1gkppggkjmgjxyjhva69s3cdb01m3f0790m4fv0"))))
    (properties `((upstream-name . "ciRcus")))
    (build-system r-build-system)
    (propagated-inputs
     (list r-annotationdbi
           r-annotationhub
           r-biocgenerics
           r-biomart
           r-data-table
           r-dbi
           r-genomeinfodb
           r-genomicfeatures
           r-genomicranges
           r-ggplot2
           r-hash
           r-iranges
           r-rcolorbrewer
           r-rmysql
           r-rtracklayer
           r-s4vectors
           r-stringr
           r-summarizedexperiment))
    (native-inputs
     (list r-knitr))
    (home-page "https://github.com/BIMSBbioinfo/ciRcus")
    (synopsis "Annotation, analysis and visualization of circRNA data")
    (description "Circus is an R package for annotation, analysis and
visualization of circRNA data.  Users can annotate their circRNA candidates
with host genes, gene featrues they are spliced from, and discriminate between
known and yet unknown splice junctions.  Circular-to-linear ratios of circRNAs
can be calculated, and a number of descriptive plots easily generated.")
    (license license:artistic2.0)))

(define-public r-domultibarheatmap
  (let ((commit "9e65afa0aa69fee631c61b7bf3e7742632c9cb95")
        (revision "1"))
    (package
      (name "r-domultibarheatmap")
      (version (git-version "0.1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/elliefewings/DoMultiBarHeatmap")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0q9mrc6md08aff6hhzlw3igvv3w7pr1wildzm8i0km9xvbi9iyy9"))))
      (properties `((upstream-name . "DoMultiBarHeatmap")))
      (build-system r-build-system)
      (propagated-inputs (list r-ggplot2 r-magrittr r-rlang r-seurat))
      (home-page "https://github.com/elliefewings/DoMultiBarHeatmap")
      (synopsis "Produce heatmap from a Seurat object with multiple annotation bars")
      (description "This package builds on Seurat's @code{Doheatmap} function
code to produce a heatmap from a Seurat object with multiple annotation
bars.")
      (license license:cc0))))

(define-public r-doubletfinder
  (let ((commit "554097ba4e2c0ed7c28dc7f0b5b75277f3a50551")
        (revision "1"))
    (package
      (name "r-doubletfinder")
      (version (git-version "2.0.3" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/chris-mcginnis-ucsf/DoubletFinder")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1q1pnqw7ry4syp04wjmvz5bws6z4vg4c340ky07lk0vp577x2773"))))
      (properties `((upstream-name . "DoubletFinder")))
      (build-system r-build-system)
      (propagated-inputs (list r-fields r-kernsmooth r-rocr))
      (home-page "https://github.com/chris-mcginnis-ucsf/DoubletFinder")
      (synopsis "Identify doublets in single-cell RNA sequencing data")
      (description
       "DoubletFinder identifies doublets by generating artificial doublets
from existing scRNA-seq data and defining which real cells preferentially
co-localize with artificial doublets in gene expression space.  Other
DoubletFinder package functions are used for fitting DoubletFinder to
different scRNA-seq datasets.  For example, ideal DoubletFinder performance in
real-world contexts requires optimal pK selection and homotypic doublet
proportion estimation.  pK selection is achieved using pN-pK parameter sweeps
and maxima identification in mean-variance-normalized bimodality coefficient
distributions.  Homotypic doublet proportion estimation is achieved by finding
the sum of squared cell annotation frequencies.")
      (license license:cc0))))

;; There have been no releases.
(define-public r-cytobackbone
  (let ((commit "4c1a0a35cc5ae1f8f516127cec92351d96fe26e7")
        (revision "1"))
    (package
      (name "r-cytobackbone")
      (version (git-version "1.0.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/tchitchek-lab/CytoBackBone")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0ahiad14zcgdk42xzw5xryic2ibn2l8lkrcdvl2b5sz2js028yb3"))))
      (properties `((upstream-name . "CytoBackBone")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-flowcore
             r-flowutils
             r-fnn
             r-ggplot2
             r-preprocesscore))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/tchitchek-lab/CytoBackBone")
      (synopsis "Merge phenotype information from different cytometric profiles")
      (description
       "This package implements an algorithm which increases the number of
simultaneously measurable markers and in this way helps with study of the
immune responses.  Thus, the present algorithm, named @code{CytoBackBone},
allows combining phenotypic information of cells from different cytometric
profiles obtained from different cytometry panels.  This computational
approach is based on the principle that each cell has its own phenotypic and
functional characteristics that can be used as an identification card.
@code{CytoBackBone} uses a set of predefined markers, that we call the
backbone, to define this identification card.  The phenotypic information of
cells with similar identification cards in the different cytometric profiles
is then merged.")
      (license license:gpl2))))

(define-public r-cytoexplorer
  (let ((commit "0efb1cc19fc701ae03905cf1b8484c1dfeb387df")
        (revision "1"))
    (package
      (name "r-cytoexplorer")
      (version (git-version "1.1.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/DillonHammill/CytoExploreR")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "1y7dadsy15i47rjmdq6ns80jzm6p0zmixll37q68ba2c7xn5pq3v"))
         (snippet
          '(delete-file
            "docs/articles/CytoExploreR_files/vis-4.20.1/vis.min.js"))))
      (properties `((upstream-name . "CytoExploreR")))
      (build-system r-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           (add-after 'unpack 'process-javascript
             (lambda* (#:key inputs #:allow-other-keys)
               (with-directory-excursion "docs/articles/CytoExploreR_files/"
                 (let ((source (search-input-file inputs "/dist/vis.js"))
                       (target "vis-4.20.1/vis.min.js"))
                   (invoke "esbuild" source "--minify"
                           (string-append "--outfile=" target)))))))))
      (propagated-inputs
       (list r-biocgenerics
             r-bslib
             r-data-table
             r-dplyr
             r-embedsom
             r-flowai
             r-flowcore
             r-flowworkspace
             r-gtools
             r-magrittr
             r-mass
             r-opencyto
             r-purrr
             r-rhandsontable
             r-robustbase
             r-rsvd
             r-rtsne
             r-shiny
             r-superheat
             r-tibble
             r-tidyr
             r-umap
             r-visnetwork))
      (native-inputs
       `(("esbuild" ,esbuild)
         ("r-knitr" ,r-knitr)
         ("js-vis"
          ,(let ((version "4.20.1"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/almende/vis")
                     (commit (string-append "v" version))))
               (file-name (git-file-name "js-vis" version))
               (sha256
                (base32
                 "09ldcqzzki5c0jlwas5992qjffqxnx6j5sl703qccfw7rg1hn469")))))))
      (home-page "https://github.com/DillonHammill/CytoExploreR")
      (synopsis "Interactive analysis of cytometry data")
      (description
       "This package has been developed under ROpenSci gudelines to integrate
conventional and cutting edge cytometry analysis tools under a unified
framework.  It aims to represent an intuitive and interactive approach to
analysing cytometry data in R.")
      (license license:gpl2))))

(define-public r-giotto
  (let ((commit "3c8067cedbf6e3112edcac2ae796de05fd9d6fe4")
        (revision "1"))
    (package
      (name "r-giotto")
      (version (git-version "1.1.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/RubD/Giotto/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1nbbqs0jk07wafshvqsdp8ds3kr9bwq88aafc5m0kdiqs7winb0d"))))
      (properties `((upstream-name . "Giotto")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-clusterr
             r-complexheatmap
             r-cowplot
             r-data-table
             r-dbscan
             r-deldir
             r-farver
             r-fitdistrplus
             r-ggdendro
             r-ggplot2
             r-ggraph
             r-ggrepel
             r-igraph
             r-irlba
             r-lfa
             r-limma
             r-magick
             r-magrittr
             r-matrix
             r-matrixstats
             r-plotly
             r-qvalue
             r-r-utils
             r-rcolorbrewer
             r-rcpp
             r-reshape2
             r-reticulate
             r-rfast
             r-rlang
             r-rtsne
             r-scales
             r-uwot))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/RubD/Giotto/")
      (synopsis "Spatial single-cell transcriptomics toolbox")
      (description
       "This package provides a toolbox to process, analyze and visualize
spatial single-cell expression data.")
      (license license:expat))))

;; Variant of r-illuminahumanmethylationepicmanifest in the
;; (gnu packages bioconductor) module.
(define-public r-illuminahumanmethylationepicmanifest-latest
  (let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3")
        (revision "1"))
    (package
      (name "r-illuminahumanmethylationepicmanifest")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url
                "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc"))))
      (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
      (build-system r-build-system)
      (home-page
       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
      (synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi")
      (description
       "This is a drop-in replacement for the
@code{IlluminaHumanMethylationEPIC} package.  It utilizes a Manifest based on
1.0B5 annotation.  As of version 0.3.0, the
@code{IlluminaHumanMethylationEPIC} package still employs the 1.0B2 annotation
manifest.  A corresponding annotation package,
@code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38}, is available to ensure
proper annotation.  The decision to maintain the same name is due to
complications in downstream processing caused by array name lookup in certain
preprocessing options.")
      (license license:artistic2.0))))

(define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
  (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
        (revision "1"))
    (package
      (name "r-illuminahumanmethylationepicanno-ilm10b5-hg38")
      (version (git-version "0.0.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url
                       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0y8fhiwmkldi57f8nq64njfgljw68cm6pb1vh44hjwcc12k48sqr"))))
      (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b5.hg38")))
      (build-system r-build-system)
      (propagated-inputs (list r-minfi))
      (home-page
       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")
      (synopsis "Illumina Human Methylation EPIC Annotation version 1.0B5")
      (description
       "This package provides a companion annotation file to the
@code{IlluminaHumanMethylationEPICmanifest} package based on the same
annotation 1.0B5.")
      (license license:artistic2.0))))

(define-public r-maxprobes
  (let ((commit "c2120dba972e12115280ef274ff80550cee5b264")
        (revision "1"))
    (package
      (name "r-maxprobes")
      (version (git-version "0.0.2" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/markgene/maxprobes")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1kij9bds2l9mwm519bzyd2608563qjlmbrayhva1s0vgml5iq9wh"))))
      (properties `((upstream-name . "maxprobes")))
      (build-system r-build-system)
      (propagated-inputs (list r-minfi r-minfidata))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/markgene/maxprobes")
      (synopsis "Methylation array cross-reactive probes")
      (description
       "The Maxprobes package collects cross-reactive probes of Illumina
methylation array 450K and EPIC/850K.")
      (license license:gpl2+))))

(define-public gffread
  ;; We cannot use the tagged release because it is not in sync with gclib.
  ;; See https://github.com/gpertea/gffread/issues/26
  (let ((commit "ba7535fcb3cea55a6e5a491d916e93b454e87fd0")
        (revision "1"))
    (package
      (name "gffread")
      (version (git-version "0.9.12" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/gpertea/gffread")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "1dl2nbcg96lxpd0drg48ssa8343nf7pw9s9mkrc4mjjmfwsin3ki"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; no check target
         #:make-flags
         (list "GCLDIR=gclib")
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (add-after 'unpack 'copy-gclib-source
             (lambda* (#:key inputs #:allow-other-keys)
               (mkdir-p "gclib")
               (copy-recursively (assoc-ref inputs "gclib-source") "gclib")
               #t))
           ;; There is no install target
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
                      (bin (string-append out "/bin")))
                 (install-file "gffread" bin))
               #t)))))
      (native-inputs
       `(("gclib-source"
          ,(let ((version "0.10.3")
                 (commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
                 (revision "1"))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/gpertea/gclib")
                     (commit commit)))
               (file-name (git-file-name "gclib" version))
               (sha256
                (base32
                 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
      (home-page "https://github.com/gpertea/gffread/")
      (synopsis "Parse and convert GFF/GTF files")
      (description
       "This package provides a GFF/GTF file parsing utility providing format
conversions, region filtering, FASTA sequence extraction and more.")
      ;; gffread is under Expat, but gclib is under Artistic 2.0
      (license (list license:expat
                     license:artistic2.0)))))

(define-public fit-sne
  (package
    (name "fit-sne")
    (version "1.2.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/KlugerLab/FIt-SNE")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1imq4577awc226wvygf94kpz156qdfw8xl0w0f7ss4w10lhmpmf5"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #false ; there are none
       #:phases
       ;; There is no build system.
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'build
           (lambda _
             (invoke "g++" "-std=c++11" "-O3"
                     "src/sptree.cpp"
                     "src/tsne.cpp"
                     "src/nbodyfft.cpp"
                     "-o" "bin/fast_tsne"
                     "-pthread" "-lfftw3" "-lm"
                     "-Wno-address-of-packed-member")))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (share (string-append out "/share/fit-sne")))
               (for-each (lambda (file) (install-file file bin))
                         (find-files "bin"))

               (substitute* "fast_tsne.R"
                 (("^FAST_TSNE_SCRIPT_DIR.*")
                  (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n")))
               (install-file "fast_tsne.R" share)))))))
    (inputs
     (list fftw))
    (home-page "https://github.com/KlugerLab/FIt-SNE")
    (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE")
    (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a
method for dimensionality reduction and visualization of high dimensional
datasets.  A popular implementation of t-SNE uses the Barnes-Hut algorithm to
approximate the gradient at each iteration of gradient descent.  This
implementation differs in these ways:

@itemize
@item Instead of approximating the N-body simulation using Barnes-Hut, we
  interpolate onto an equispaced grid and use FFT to perform the convolution.
@item Instead of computing nearest neighbors using vantage-point trees, we
  approximate nearest neighbors using the Annoy library.  The neighbor lookups
  are multithreaded to take advantage of machines with multiple cores.
@end itemize
")
    ;; See LICENSE.txt for details on what license applies to what files.
    (license (list license:bsd-4 license:expat license:asl2.0))))

(define-public python-scanpy
  (package
    (name "python-scanpy")
    (version "1.9.6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/theislab/scanpy")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "12rz0a9151fkry6ws1a8p5wnc4n5qbjl6xlynj7kxy223iz8isds"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             ;; Plot tests that fail.
             (string-append "not test_clustermap"
                            " and not test_dotplot_matrixplot_stacked_violin"
                            " and not test_paga_compare"
                            " and not test_paga_path"
                            " and not test_paga_pie"
                            " and not test_paga_plots"
                            " and not test_violin"
                            " and not test_scatter_no_basis_per_obs"

                            ;; Type mismatch
                            " and not test_obs_df"
                            " and not test_var_df"

                            ;; Minor accuracy problem
                            " and not test_consistency[morans_i-allclose]"

                            ;; These try to connect to the network
                            " and not test_scrublet_plots"
                            " and not test_plot_rank_genes_groups_gene_symbols"
                            " and not test_pca_n_pcs"
                            " and not test_pca_chunked"
                            " and not test_pca_sparse"
                            " and not test_pca_reproducible"))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'pretend-version
             (lambda _
               (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
           (add-after 'unpack 'delete-bad-tests
             (lambda _
               ;; These tests require Internet access.
               (delete-file-recursively "scanpy/tests/notebooks")
               (delete-file "scanpy/tests/test_clustering.py")
               (delete-file "scanpy/tests/test_datasets.py")
               (delete-file "scanpy/tests/test_normalization.py")
               (delete-file "scanpy/tests/test_score_genes.py")
               (delete-file "scanpy/tests/test_highly_variable_genes.py")

               ;; TODO: I can't get the plotting tests to work, even with Xvfb.
               (delete-file "scanpy/tests/test_embedding_plots.py")
               (delete-file "scanpy/tests/test_preprocessing.py")
               (delete-file "scanpy/tests/test_read_10x.py")

               ;; These two fail with "ValueError: I/O operation on closed file."
               (delete-file "scanpy/tests/test_neighbors_key_added.py")

               ;; The following tests requires 'scanorama', which isn't
               ;; packaged yet.
               (delete-file "scanpy/tests/external/test_scanorama_integrate.py")

               (setenv "PYTHONPATH"
                       (string-append (getcwd) ":"
                                      #$(this-package-native-input "python-anndata:source") ":"
                                      (getenv "GUIX_PYTHONPATH")))))
           ;; Numba needs a writable dir to cache functions.
           (add-before 'check 'set-numba-cache-dir
             (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs
     (list python-anndata
           python-dask
           python-h5py
           python-igraph
           python-joblib
           python-legacy-api-wrap
           python-louvain
           python-matplotlib
           python-natsort
           python-networkx
           python-numba
           python-packaging
           python-pandas
           python-patsy
           python-scikit-learn
           python-scipy
           python-seaborn
           python-session-info
           python-sinfo
           python-statsmodels
           python-tables
           python-pytoml
           python-tqdm
           python-umap-learn))
    (native-inputs
     `(;; This package needs anndata.tests, which is not installed.
       ("python-anndata:source" ,(package-source python-anndata))
       ("python-flit" ,python-flit)
       ("python-hatchling" ,python-hatchling)
       ("python-hatch-vcs" ,python-hatch-vcs)
       ("python-leidenalg" ,python-leidenalg)
       ("python-pytest" ,python-pytest)
       ("python-pytest-nunit" ,python-pytest-nunit)
       ("python-setuptools-scm" ,python-setuptools-scm)))
    (home-page "https://github.com/theislab/scanpy")
    (synopsis "Single-Cell Analysis in Python")
    (description "Scanpy is a scalable toolkit for analyzing single-cell gene
expression data.  It includes preprocessing, visualization, clustering,
pseudotime and trajectory inference and differential expression testing.  The
Python-based implementation efficiently deals with datasets of more than one
million cells.")
    (license license:bsd-3)))

(define-public python-bbknn
  (package
    (name "python-bbknn")
    (version "1.6.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "bbknn" version))
       (sha256
        (base32
         "06q43cpi7wi6f2d2jqs8f9rbd94pg1hh7978gm92mi9gvzbaj08w"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #f                       ;no tests are included
      #:phases
      '(modify-phases %standard-phases
         ;; Numba needs a writable dir to cache functions.
         (add-before 'check 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs
     (list python-annoy
           python-cython
           python-numpy
           python-pandas
           python-pynndescent
           python-scikit-learn
           python-scipy
           python-umap-learn))
    (native-inputs (list python-flit-core))
    (home-page "https://github.com/Teichlab/bbknn")
    (synopsis "Batch balanced KNN")
    (description "BBKNN is a batch effect removal tool that can be directly
used in the Scanpy workflow.  It serves as an alternative to
@code{scanpy.api.pp.neighbors()}, with both functions creating a neighbour
graph for subsequent use in clustering, pseudotime and UMAP visualisation.  If
technical artifacts are present in the data, they will make it challenging to
link corresponding cell types across different batches.  BBKNN actively
combats this effect by splitting your data into batches and finding a smaller
number of neighbours for each cell within each of the groups.  This helps
create connections between analogous cells in different batches without
altering the counts or PCA space.")
    (license license:expat)))

(define-public python-drep
  (package
    (name "python-drep")
    (version "3.2.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "drep" version))
       (sha256
        (base32
         "08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77"))))
    (build-system python-build-system)
    (propagated-inputs
     (list python-biopython
           python-matplotlib
           python-numpy
           python-pandas
           python-pytest
           python-scikit-learn
           python-seaborn
           python-tqdm))
    (home-page "https://github.com/MrOlm/drep")
    (synopsis "De-replication of microbial genomes assembled from multiple samples")
    (description
     "dRep is a Python program for rapidly comparing large numbers of genomes.
dRep can also \"de-replicate\" a genome set by identifying groups of highly
similar genomes and choosing the best representative genome for each genome
set.")
    (license license:expat)))

(define-public instrain
  (package
    (name "instrain")
    (version "1.5.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "inStrain" version))
       (sha256
        (base32
         "05w1lw75x4lwkzg4qpi055g7hdjp9rnc4ksbxg2hfgksq9djk0hx"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-relative-imports
           (lambda _
             (substitute* "docker/run_instrain.py"
               (("from s3_utils")
                "from .s3_utils")
               (("from job_utils")
                "from .job_utils")))))))
    (inputs
     (list python-biopython-1.73
           python-boto3
           python-h5py
           python-lmfit
           python-matplotlib
           python-networkx
           python-numba
           python-numpy
           python-pandas
           python-psutil
           python-pysam
           python-scikit-learn
           python-seaborn
           python-tqdm
           ;; drep is needed for deprecated plot utilities
           python-drep))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/MrOlm/inStrain")
    (synopsis "Calculation of strain-level metrics")
    (description
     "inStrain is a Python program for analysis of co-occurring genome
populations from metagenomes that allows highly accurate genome comparisons,
analysis of coverage, microdiversity, and linkage, and sensitive SNP detection
with gene localization and synonymous non-synonymous identification.")
    ;; The tool itself says that the license is "MIT", but the repository
    ;; contains a LICENSE file with the GPLv3.
    ;; See https://github.com/MrOlm/inStrain/issues/51
    (license license:expat)))

(define-public gffcompare
  (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
        (revision "1"))
    (package
      (name "gffcompare")
      (version (git-version "0.10.15" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/gpertea/gffcompare/")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f                    ; no check target
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (add-before 'build 'copy-gclib-source
             (lambda* (#:key inputs #:allow-other-keys)
               (mkdir "../gclib")
               (copy-recursively
                (assoc-ref inputs "gclib-source") "../gclib")
               #t))
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                 (install-file "gffcompare" bin)
                 #t))))))
      (native-inputs
       `(("gclib-source" ; see 'README.md' of gffcompare
          ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
                 (revision "1")
                 (name "gclib")
                 (version (git-version "0.10.3" revision commit)))
             (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/gpertea/gclib/")
                     (commit commit)))
               (file-name (git-file-name name version))
               (sha256
                (base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
      (home-page "https://github.com/gpertea/gffcompare/")
      (synopsis "Tool for comparing or classifing transcripts of RNA-Seq")
      (description
       "@code{gffcompare} is a tool that can:
@enumerate
@item compare and evaluate the accuracy of RNA-Seq transcript assemblers
(Cufflinks, Stringtie);
@item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g.
resulted from assembly of different samples);
@item classify transcripts from one or multiple GTF/GFF3 files as they relate to
reference transcripts provided in a annotation file (also in GTF/GFF3 format).
@end enumerate")
      (license
       (list
        license:expat                   ;license for gffcompare
        license:artistic2.0)))))        ;license for gclib

(define-public intervaltree
  (let ((commit "b90527f9e6d51cd36ecbb50429e4524d3a418ea5"))
    (package
      (name "intervaltree")
      (version (git-version "0.0.0" "1" commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://github.com/ekg/intervaltree/")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32 "0rgv6q5fl4x5d74n6p5wvdna6zmbdbqpb4jqqh6vq3670gn08xad"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f                    ; No tests.
         #:make-flags
         ,#~(list (string-append "PREFIX=" #$output) "DESTDIR=\"\"")
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)))) ; There is no configure phase.
      (home-page "https://github.com/ekg/intervaltree")
      (synopsis "Minimal C++ interval tree implementation")
      (description "An interval tree can be used to efficiently find a set of
numeric intervals overlapping or containing another interval.  This library
provides a basic implementation of an interval tree using C++ templates,
allowing the insertion of arbitrary types into the tree.")
      (license license:expat))))

(define-public python-intervaltree
  (package
    (name "python-intervaltree")
    (version "3.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "intervaltree" version))
       (sha256
        (base32
         "0bcm6c6r4ck9nfj9xwz4rm2swc5lrjvmw3lyl6rgj639jf41nawh"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; pytest seems to have a check to make sure the user is testing
         ;; their checked-out code and not an installed, potentially
         ;; out-of-date copy. This is harmless here, since we just installed
         ;; the package, so we disable the check to avoid skipping tests
         ;; entirely.
         (add-before 'check 'import-mismatch-error-workaround
           (lambda _
             (setenv "PY_IGNORE_IMPORTMISMATCH" "1")
             #t)))))
    (propagated-inputs
     (list python-sortedcontainers))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/chaimleib/intervaltree")
    (synopsis "Editable interval tree data structure")
    (description
     "This package provides a mutable, self-balancing interval tree
implementation for Python.  Queries may be by point, by range overlap, or by
range envelopment.  This library was designed to allow tagging text and time
intervals, where the intervals include the lower bound but not the upper
bound.")
    (license license:asl2.0)))

(define-public python-pypairix
  (package
    (name "python-pypairix")
    (version "0.3.7")
    ;; The tarball on pypi does not include the makefile to build the
    ;; programs.
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/4dn-dcic/pairix")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1snr3lrmsld8sy77ng6ba6wcmd33xjccf1l2f3m6pi29xis9nd6p"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'build-programs
           (lambda _ (invoke "make")))
         (add-after 'install 'install-programs
           (lambda* (#:key outputs #:allow-other-keys)
             (copy-recursively "bin" (string-append
                                      (assoc-ref outputs "out")
                                      "/bin"))
             #t)))))
    (inputs
     (list zlib))
    (home-page "https://github.com/4dn-dcic/pairix")
    (synopsis "Support for querying pairix-indexed bgzipped text files")
    (description
     "Pypairix is a Python module for fast querying on a pairix-indexed
bgzipped text file that contains a pair of genomic coordinates per line.")
    (license license:expat)))

(define-public python-pyrodigal
  (package
    (name "python-pyrodigal")
    (version "3.3.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/althonos/pyrodigal")
             (commit (string-append "v" version))
             (recursive? #t)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "10vxbm9i33wari0ifsr78xnfn7d0yqwzqpc5pchirjflf1mmnr6w"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:modules '((ice-9 ftw)
                  (srfi srfi-1)
                  (srfi srfi-26)
                  (guix build utils)
                  (guix build pyproject-build-system))
      #:phases
      #~(modify-phases %standard-phases
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (let ((cwd (getcwd))
                      (libdir (find (cut string-prefix? "lib." <>)
                                    (scandir "build"))))
                  (with-directory-excursion (string-append cwd "/build/" libdir)
                    (invoke "python3" "-m" "unittest" "pyrodigal.tests" "-vv")))))))))
    (propagated-inputs (list python-archspec python-importlib-resources))
    (native-inputs (list python-cython-3 python-mock python-unittest2))
    (home-page "https://github.com/althonos/pyrodigal")
    (synopsis "Cython bindings and Python interface for Prodigal")
    (description
     "This package offers Cython bindings and a Python interface for Prodigal.
 Prodigal is an ORF finder designed for both genomes and metagenomes.")
    (license license:gpl3)))

(define-public python-pyfaidx
  (package
    (name "python-pyfaidx")
    (version "0.7.2.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pyfaidx" version))
              (sha256
               (base32
                "182ia2zg026lgphv68agxm9imw7649z9pdhfn8zkalrxkq5d5w1h"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      ;; These tests require the download of large fasta.gz files.
      '(list "--ignore=tests/test_Fasta_bgzip.py")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-version
            (lambda _
              (substitute* "pyproject.toml"
                (("dynamic = \\[\"version\"\\]")
                 (string-append "version = \"" #$version "\""))))))))
    (native-inputs
     (list (libc-utf8-locales-for-target)         ;tests need "en_US.utf8"
           python-fsspec
           python-mock
           python-numpy
           python-pytest
           python-pytest-cov))
    (home-page "http://mattshirley.com")
    (synopsis "Random access to fasta subsequences")
    (description
     "This package provides procedures for efficient pythonic random access to
fasta subsequences.")
    (license license:bsd-3)))

(define-public python-cooler
  (package
    (name "python-cooler")
    (version "0.9.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cooler" version))
       (sha256
        (base32
         "0qqb0i5449r6w871klsbjzxsjhdkpsaas3hvs9f1hc7ssrkf1vi1"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             (string-append
              ;; These tests download files from the internet.
              "not test_fetch_chromsizes"
              " and not test_roundtrip"
              ;; This test depends on ipytree, which contains a lot of
              ;; minified JavaScript.
              " and not test_print_trees"))))
    (propagated-inputs
     (list python-asciitree
           python-biopython
           python-click
           python-cytoolz
           python-dask
           python-h5py
           python-multiprocess
           python-numpy
           python-pandas
           python-pyfaidx
           python-pypairix
           python-pysam
           python-pyyaml
           python-scipy
           python-simplejson))
    (native-inputs
     (list python-coverage
           python-hatchling
           python-isort
           python-pytest
           python-pytest-cov))
    ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
    (home-page "https://github.com/open2c/cooler")
    (synopsis "Sparse binary format for genomic interaction matrices")
    (description
     "Cooler is a support library for a sparse, compressed, binary persistent
storage format, called @code{cool}, used to store genomic interaction data,
such as Hi-C contact matrices.")
    (license license:bsd-3)))

(define-public python-cooltools
  (package
    (name "python-cooltools")
    (version "0.7.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "cooltools" version))
              (sha256
               (base32
                "076fgqzf6453cx5zs32vz0f5yvfg53w8ayq9s79jssy7gj2x89lb"))))
    (build-system pyproject-build-system)
    (native-inputs
     (list python-cython
           python-pytest))
    (propagated-inputs
     (list python-bioframe
           python-click
           python-cooler
           python-joblib
           python-matplotlib
           python-multiprocess
           python-numba
           python-numpy
           python-pandas
           python-scikit-image
           python-scikit-learn
           python-scipy))
    (home-page "https://github.com/open2c/cooltools")
    (synopsis
     "Analysis tools for genomic interaction data stored in .cool format")
    (description
     "This package provides necessary tools for the analysis of the genomic
interaction data stored in @code{.cool} format.  This collection of tools
includes operations like compartment, insulation or peak calling.")
    (license license:expat)))

(define-public python-hicmatrix
  (package
    (name "python-hicmatrix")
    (version "17.1")
      (source
        (origin
          ;;Pypi sources do not contain any test
          (method git-fetch)
          (uri (git-reference
                 (url "https://github.com/deeptools/HiCMatrix")
                 (commit version)))
          (file-name (git-file-name name version))
          (sha256
            (base32
             "14gq7r9b64ff56l5f8h8zc2i2y3xri646jl0anb74japqxrwvlna"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-cooler
           python-intervaltree
           python-numpy
           python-pandas
           python-scipy
           python-tables))
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/deeptools/HiCMatrix/")
    (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks")
    (description
     "This helper package implements the @code{HiCMatrix} class for
the HiCExplorer and pyGenomeTracks packages.")
    (license license:gpl3+)))

(define-public python-hicexplorer
  (package
    (name "python-hicexplorer")
    (version "3.7.4")
    (source
     (origin
       ;; The latest version is not available on Pypi.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/deeptools/HiCExplorer")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1cjr9l0vcngd0f4dmar388ri1ah1bqybnn53jc85xwh07wfacq7l"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "hicexplorer/test/general/"
             "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py"
             "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py"
             "-k"
             (string-append
              ;; Unknown chromosome: ChrX
              "not test_build_matrix_restrictionCutFile_two"
              ;; fixture 'keepSelfLigation' not found
              " and not test_build_matrix_restrictionCutFile_six"
              ;; ValueError: object dtype is not supported by sparse matrices
              " and not test_hic_transfer_obs_exp_perChromosome"

              ;; No KR balancing available
              " and not test_correct_matrix_KR_partial_cool"
              " and not test_correct_matrix_KR_cool"
              " and not test_correct_matrix_KR_H5"))
      #:phases
      #~(modify-phases %standard-phases
          ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23
          (add-after 'unpack 'remove-dependency-on-krbalancing
            (lambda _
              (substitute* "hicexplorer/hicCorrectMatrix.py"
                (("from krbalancing import.*") "")
                (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent)
                 (string-append m "\n"
                                indent "log.error('krbalancing not available')\n"
                                indent "exit(1)")))
              (substitute* "setup.py"
                (("\"krbalancing >= 0.0.5\",") ""))
              (substitute* "requirements.txt"
                (("krbalancing >= 0.0.5") ""))))
          (add-after 'unpack 'fix-references
            (lambda _
              (let ((site (string-append #$output "/lib/python"
                                         #$(version-major+minor
                                            (package-version python))
                                         "/site-packages")))
                (substitute* "hicexplorer/lib/tadClassifier.py"
                  (("model_location = site.getsitepackages\\(\\)\\[0\\]")
                   (string-append "model_location = \"" site "\""))))
              (substitute* "hicexplorer/hicFindRestSite.py"
                (("subprocess.check_output\\(\\[\"cat\"")
                 (string-append "subprocess.check_output([\""
                                (which "cat") "\""))
                (("cmd = 'sort -k1")
                 (string-append "cmd = '" (which "sort") " -k1")))))
          ;; The tests aim to detect available memory and run more tests when
          ;; there is more available memory.  Let's run them deterministically
          ;; instead and don't run any tests that require more than 1GB of
          ;; RAM.
          (add-after 'unpack 'run-only-low-mem-tests
            (lambda _
              (with-directory-excursion "hicexplorer/test"
                (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py"
                               "trivial_runs/test_hicBuildMatrix_trivial_runs.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py"
                               "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py"
                               "general/test_hicDifferentialTAD.py"
                               "general/test_hicDetectLoops.py"
                               "general/test_hicPlotMatrix.py"
                               "general/test_hicHyperoptDetectLoops.py"
                               "general/test_hicCreateThresholdFile.py"
                               "general/test_hicMergeDomains.py"
                               "general/test_hicHyperoptDetectLoopsHiCCUPS.py"
                               "general/test_hicAggregateContacts.py"
                               "general/test_hicInterIntraTAD.py")
                  (("^memory =.*") "memory = 1\n"))))))))
    (propagated-inputs
     (list python-biopython
           python-cleanlab
           python-cooler
           python-fit-nbinom
           python-future
           python-graphviz
           python-hic2cool
           python-hicmatrix
           python-hyperopt
           python-imbalanced-learn
           python-intervaltree
           python-ipykernel
           python-jinja2
           python-matplotlib
           python-numpy
           python-pandas
           python-psutil
           python-pybedtools
           python-pybigwig
           python-pygenometracks
           python-pysam
           python-scikit-learn
           python-scipy
           python-tables
           python-tqdm
           python-unidecode))
    (native-inputs
     (list graphviz)) ;for hicexplorer/test/test_compute_function.py
    (home-page "https://hicexplorer.readthedocs.io")
    (synopsis "Process, analyze and visualize Hi-C data")
    (description
     "HiCExplorer is a powerful and easy to use set of tools to process,
normalize and visualize Hi-C data.  HiCExplorer facilitates the creation of
contact matrices, correction of contacts, TAD detection, A/B compartments,
merging, reordering or chromosomes, conversion from different formats
including cooler and detection of long-range contacts.  Moreover, it allows
the visualization of multiple contact matrices along with other types of data
like genes, compartments, ChIP-seq coverage tracks (and in general any type of
genomic scores), long range contacts and the visualization of viewpoints.")
    (license license:gpl3)))

(define-public python-pygenometracks
  (package
    (name "python-pygenometracks")
    (version "3.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pyGenomeTracks" version))
       (sha256
        (base32
         "1l7smg2gc1vm2181lzmdnywb11gp6s6z6j444dbsigv65car8z8p"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #f                       ;there are none
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "setup.py"
               (("matplotlib ==3.1.1")
                "matplotlib >=3.1.1"))))
         (add-after 'unpack 'remove-invalid-syntax
           (lambda _
             (substitute* "setup.py"
               ((".\\*,") ",")))))))
    (propagated-inputs
     (list python-future
           python-gffutils
           python-hicmatrix
           python-intervaltree
           python-matplotlib
           python-numpy
           python-pybigwig
           python-pysam
           python-tqdm))
    (native-inputs
     (list python-pytest))
    (home-page "https://pygenometracks.readthedocs.io")
    (synopsis "Program and library to plot beautiful genome browser tracks")
    (description
     "This package aims to produce high-quality genome browser tracks that
are highly customizable.  Currently, it is possible to plot: bigwig, bed (many
options), bedgraph, links (represented as arcs), and Hi-C matrices.
pyGenomeTracks can make plots with or without Hi-C data.")
    (license license:gpl3+)))

(define-public python-iced
  (package
    (name "python-iced")
    (version "0.5.8")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "iced" version))
       (sha256
        (base32
         "1avcjmpyyvhgbj5qca4l70ipiz7j3xmcw9p6rd9c06j99faa0r71"))))
    (build-system python-build-system)
    (arguments `(#:tests? #false)) ; there are none
    (propagated-inputs
     (list python-numpy python-pandas python-scipy python-scikit-learn))
    (home-page "https://github.com/hiclib/iced")
    (synopsis "ICE normalization")
    (description "This is a package for normalizing Hi-C contact counts
efficiently.")
    (license license:bsd-3)))

(define-public python-hic2cool
  (package
    (name "python-hic2cool")
    (version "0.8.3")
    ;; pypi sources do not contain the test_data directory and no test can be
    ;; run
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/4dn-dcic/hic2cool")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; Two of the test-data files need to be writable.
         (add-after 'unpack 'make-test-data-writable
           (lambda _
             (for-each make-file-writable
                       (list "test_data/hic2cool_0.4.2_single_res.cool"
                             "test_data/hic2cool_0.7.0_multi_res.mcool"))))
         ;; See https://github.com/4dn-dcic/hic2cool/issues/58
         (add-after 'unpack 'fix-incompatibility-with-h5py-3
           (lambda _
             (substitute* "test.py"
               (("h5py.File\\(fname\\)") "h5py.File(fname, 'r')"))
             (substitute* "hic2cool/hic2cool_updates.py"
               (("h5py.File\\(writefile\\)")
                "h5py.File(writefile, 'a')"))))
         ;; These two tests fail for unknown reasons.
         (add-after 'unpack 'disable-broken-tests
           (lambda _
             (substitute* "test.py"
               (("def test_convert") "def _test_convert")))))))
    (propagated-inputs
     (list python-cooler python-h5py python-numpy python-pandas
           python-scipy))
    (home-page "https://github.com/4dn-dcic/hic2cool")
    (synopsis "Converter for .hic and .cool files")
    (description
     "This package provides a converter between @code{.hic} files (from
juicer) and single-resolution or multi-resolution @code{.cool} files (for
cooler).  Both @code{hic} and @code{cool} files describe Hi-C contact
matrices.")
    (license license:expat)))

(define-public python-scanorama
  (package
    (name "python-scanorama")
    (version "1.7.2")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "scanorama" version))
              (sha256
               (base32
                "0il7bf4c7vli2dm2jx7dskh3ymgv8nmk0y90jzgfrnqjzh250x5w"))))
    (build-system python-build-system)
    (propagated-inputs
     (list python-annoy
           python-fbpca
           python-geosketch
           python-intervaltree
           python-matplotlib
           python-numpy
           python-scikit-learn
           python-scipy))
    (home-page "https://github.com/brianhie/scanorama")
    (synopsis "Panoramic stitching of heterogeneous single cell transcriptomic data")
    (description
     "Scanorama enables batch-correction and integration of heterogeneous
scRNA-seq datasets, which is described in the paper \"Efficient integration of
heterogeneous single-cell transcriptomes using Scanorama\" by Brian Hie, Bryan
Bryson, and Bonnie Berger.")
    (license license:expat)))

(define-public r-pore
  (package
    (name "r-pore")
    (version "0.24")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/rpore/" version
                       "/poRe_" version ".tar.gz"))
       (sha256
        (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
    (properties `((upstream-name . "poRe")))
    (build-system r-build-system)
    (propagated-inputs
     (list r-bit64 r-data-table r-rhdf5 r-shiny r-svdialogs))
    (home-page "https://sourceforge.net/projects/rpore/")
    (synopsis "Visualize Nanopore sequencing data")
    (description
     "This package provides graphical user interfaces to organize and visualize Nanopore
sequencing data.")
    ;; This is free software but the license variant is unclear:
    ;; <https://github.com/mw55309/poRe_docs/issues/10>.
    (license license:bsd-3)))

(define-public r-xbioc
  (let ((revision "1")
        (commit "6ff0670a37ab3036aaf1d94aa4b208310946b0b5"))
    (package
      (name "r-xbioc")
      (version (git-version "0.1.16" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/renozao/xbioc")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0w8bsq5myiwkfhh83nm6is5ichiyvwa1axx2szvxnzq39x6knf66"))))
      (build-system r-build-system)
      (propagated-inputs
       (list r-annotationdbi
             r-assertthat
             r-biobase
             r-biocmanager
             r-digest
             r-pkgmaker
             r-plyr
             r-reshape2
             r-stringr))
      (home-page "https://github.com/renozao/xbioc/")
      (synopsis "Extra base functions for Bioconductor")
      (description "This package provides extra utility functions to perform
common tasks in the analysis of omics data, leveraging and enhancing features
provided by Bioconductor packages.")
      (license license:gpl3+))))

(define-public r-cssam
  (let ((revision "1")
        (commit "9ec58c982fa551af0d80b1a266890d92954833f2"))
    (package
      (name "r-cssam")
      (version (git-version "1.4" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/shenorrLab/csSAM")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3"))))
      (build-system r-build-system)
      (propagated-inputs
       (list r-formula
             r-ggplot2
             r-pkgmaker
             r-plyr
             r-rngtools
             r-scales))
      (home-page "https://github.com/shenorrLab/csSAM/")
      (synopsis "Cell type-specific statistical analysis of microarray")
      (description "This package implements the method csSAM that computes
cell-specific differential expression from measured cell proportions using
SAM.")
      ;; Any version
      (license license:lgpl2.1+))))

(define-public r-bseqsc
  (let ((revision "1")
        (commit "fef3f3e38dcf3df37103348b5780937982b43b98"))
    (package
      (name "r-bseqsc")
      (version (git-version "1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/shenorrLab/bseqsc")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8"))))
      (build-system r-build-system)
      (propagated-inputs
       (list r-abind
             r-annotationdbi
             r-biobase
             r-cssam
             r-dplyr
             r-e1071
             r-edger
             r-ggplot2
             r-nmf
             r-openxlsx
             r-pkgmaker
             r-plyr
             r-preprocesscore
             r-rngtools
             r-scales
             r-stringr
             r-xbioc))
      (home-page "https://github.com/shenorrLab/bseqsc")
      (synopsis "Deconvolution of bulk sequencing experiments using single cell data")
      (description "BSeq-sc is a bioinformatics analysis pipeline that
leverages single-cell sequencing data to estimate cell type proportion and
cell type-specific gene expression differences from RNA-seq data from bulk
tissue samples.  This is a companion package to the publication \"A
single-cell transcriptomic map of the human and mouse pancreas reveals inter-
and intra-cell population structure.\" Baron et al. Cell Systems (2016)
@url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
      (license license:gpl2+))))

(define-public porechop
  ;; The recommended way to install is to clone the git repository
  ;; https://github.com/rrwick/Porechop#installation
  (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
        (revision "1"))
    (package
      (name "porechop")
      (version (git-version "0.2.3" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/rrwick/Porechop")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
      (build-system python-build-system)
      (home-page "https://github.com/rrwick/porechop")
      (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
      (description
       "The porechop package is a tool for finding and removing adapters from Oxford
Nanopore reads.  Adapters on the ends of reads are trimmed off, and when a read
has an adapter in its middle, it is treated as chimeric and chopped into
separate reads.  Porechop performs thorough alignments to effectively find
adapters, even at low sequence identity.  Porechop also supports demultiplexing
of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR
Barcoding Kit or Rapid Barcoding Kit.")
      (license license:gpl3+))))

(define-public jamm
  (package
    (name "jamm")
    (version "1.0.7.6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/mahmoudibrahim/JAMM")
             (commit (string-append "JAMMv" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (delete 'build)
          (replace 'install
            (lambda _
              (let ((libexec (string-append #$output "/libexec/jamm"))
                    (bin (string-append #$output "/bin")))
                (substitute* '("JAMM.sh"
                               "SignalGenerator.sh")
                  (("^sPath=.*")
                   (string-append "sPath=\"" libexec "\"\n")))
                (for-each (lambda (file)
                            (install-file file libexec))
                          (list "bincalculator.r"
                                "peakfinder.r"
                                "peakhelper.r"
                                "signalmaker.r"
                                "xcorr.r"
                                "xcorrhelper.r"
                                ;; Perl scripts
                                "peakfilter.pl"
                                "readshifter.pl"))

                (for-each
                 (lambda (script)
                   (chmod script #o555)
                   (install-file script bin)
                   (wrap-program (string-append bin "/" script)
                     `("PATH" ":" prefix
                       (,(string-append #$(this-package-input "coreutils") "/bin")
                        ,(string-append #$(this-package-input "gawk") "/bin")
                        ,(string-append #$(this-package-input "perl") "/bin")
                        ,(string-append #$(this-package-input "r-minimal") "/bin")))
                     `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
                     `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
                 (list "JAMM.sh" "SignalGenerator.sh"))))))))
    (inputs
     (list bash
           coreutils
           gawk
           perl
           r-minimal
           ;;("r-parallel" ,r-parallel)
           r-signal
           r-mclust))
    (home-page "https://github.com/mahmoudibrahim/JAMM")
    (synopsis "Peak finder for NGS datasets")
    (description
     "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
boundaries accurately.  JAMM is applicable to both broad and narrow
datasets.")
    (license license:gpl3+)))

(define-public ngless
  (package
    (name "ngless")
    (version "1.5.0")
    (source (origin
              (method url-fetch)
              (uri (hackage-uri "NGLess" version))
              (sha256
               (base32
                "0pljyrlpr9r3cl5311dhgxdl8y40szyi4vprn34i3piy0qrldymi"))))
    (build-system haskell-build-system)
    (arguments
     `(#:haddock? #f
       #:phases
       (modify-phases %standard-phases
         (add-before 'configure 'update-constraints
           (lambda _
             (substitute* "NGLess.cabal"
               (("\\b(base)\\s+[^,]+" all dep)
                dep))))
         (add-after 'unpack 'create-Versions.hs
           (lambda _
             (substitute* "NGLess/Dependencies/Versions.hs"
               (("bwaVersion = .+")
                (string-append "bwaVersion = \""
                               ,(package-version bwa) "\""))
               (("samtoolsVersion = .+")
                (string-append "samtoolsVersion = \""
                               ,(package-version samtools) "\""))
               (("prodigalVersion = .+")
                (string-append "prodigalVersion = \""
                               ,(package-version prodigal) "\""))
               (("megahitVersion = .+")
                (string-append "megahitVersion = \""
                               ,(package-version megahit) "\""))
               (("minimap2Version = .+")
                (string-append "minimap2Version = \""
                               ,(package-version minimap2) "\"")))))
         ;; See NGLess/FileManagement.hs.
         (add-after 'install 'wrap-program
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
                      (bwa (search-input-file inputs "/bin/bwa"))
                      (samtools (search-input-file inputs "/bin/samtools"))
                      (prodigal (search-input-file inputs "/bin/prodigal"))
                      (minimap2 (search-input-file inputs "/bin/minimap2"))
                      (megahit (search-input-file inputs "/bin/megahit")))
                 (wrap-program (string-append out "/bin/ngless")
                   `("NGLESS_BWA_BIN" " " = (,bwa))
                   `("NGLESS_SAMTOOLS_BIN" " " = (,samtools))
                   `("NGLESS_PRODIGAL_BIN" " " = (,prodigal))
                   `("NGLESS_MINIMAP2_BIN" " " = (,minimap2))
                   `("NGLESS_MEGAHIT_BIN" " " = (,megahit))))))
          ;; Sanity check.
          (add-after 'wrap-program 'check-install
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((ngless (string-append (assoc-ref outputs "out") "/bin/ngless")))
                 (invoke ngless "--check-install"))))
          (add-after 'register 'remove-libraries
            (lambda* (#:key outputs #:allow-other-keys)
              (delete-file-recursively (string-append (assoc-ref outputs "out") "/lib")))))))
    (inputs (list bash-minimal
                  prodigal
                  bwa
                  samtools
                  minimap2
                  megahit
                  ghc-missingh
                  ghc-aeson
                  ghc-ansi-terminal
                  ghc-async
                  ghc-atomic-write
                  ghc-bytestring-lexing
                  ghc-conduit
                  ghc-conduit-algorithms
                  ghc-conduit-extra
                  ghc-configurator
                  ghc-convertible
                  ghc-data-default
                  ghc-edit-distance
                  ghc-either
                  ghc-errors
                  ghc-extra
                  ghc-file-embed
                  ghc-filemanip
                  ghc-hashable
                  ghc-hashtables
                  ghc-hostname
                  ghc-http-client
                  ghc-http-conduit
                  ghc-inline-c
                  ghc-inline-c-cpp
                  ghc-int-interval-map
                  ghc-network
                  ghc-optparse-applicative
                  ghc-primitive
                  ghc-random-shuffle
                  ghc-regex
                  ghc-resourcet
                  ghc-safe
                  ghc-stm-chans
                  ghc-stm-conduit
                  ghc-strict
                  ghc-tar
                  ghc-tar-conduit
                  ghc-unix-compat
                  ghc-unliftio
                  ghc-unliftio-core
                  ghc-vector
                  ghc-vector-algorithms
                  ghc-yaml
                  ghc-zlib
                  ghc-bzlib-conduit
                  ghc-double-conversion
                  ghc-safeio))
    (propagated-inputs
     (list r-r6 r-hdf5r r-iterators r-itertools r-matrix))
    (native-inputs (list ghc-hunit
                         ghc-quickcheck
                         ghc-tasty
                         ghc-tasty-hunit
                         ghc-tasty-quickcheck
                         ghc-tasty-th))
    (home-page "https://ngless.embl.de/")
    (synopsis "DSL for processing next-generation sequencing data")
    (description "Ngless is a domain-specific language for
@dfn{next-generation sequencing} (NGS) data processing.")
    (license license:expat)))

(define-public ghc-int-interval-map
  (let ((commit "678763de7fe6d7fa3f1c44b32d18ce58670270f4")
        (revision "1"))
    (package
      (name "ghc-int-interval-map")
      (version "0.0.0.0")
      (source
        (origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/ngless-toolkit/interval-to-int.git")
                 (commit commit)))
           (file-name (git-file-name name version))
          (sha256 (base32 "0fd728b5if89vj5j4f9y7k0b2xv2ycz5a21iy15wbdcf5bhim7i8"))))
      (build-system haskell-build-system)
      (inputs
        (list ghc-either ghc-primitive ghc-vector ghc-vector-algorithms))
      (native-inputs
        (list ghc-hedgehog
              ghc-tasty
              ghc-tasty-hedgehog
              ghc-tasty-hunit
              ghc-tasty-quickcheck
              ghc-tasty-th))
      (home-page "https://github.com/luispedro/interval-to-int#readme")
      (synopsis "Interval map structure in Haskell")
      (description "An interval map structure that is optimized for low
memory (each interval is represented by about 3 words + whatever the
cargo is) and has semantics that are appropriate for genomic intervals
(namely, intervals can overlap and queries will return all matches
together). It also designed to be used in two phases: a construction
phase + query phase).")
      (license license:expat))))

(define-public filtlong
  ;; The recommended way to install is to clone the git repository
  ;; https://github.com/rrwick/Filtlong#installation
  ;; and the lastest release is more than nine months old
  (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
        (revision "1"))
    (package
      (name "filtlong")
      (version (git-version "0.2.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/rrwick/Filtlong")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
      (build-system gnu-build-system)
      (arguments
       (list
        #:tests? #f                    ; no check target
        #:phases
        #~(modify-phases %standard-phases
            (delete 'configure)
            (replace 'install
              (lambda _
                (let ((bin (string-append #$output "/bin"))
                      (scripts (string-append #$output "/share/filtlong/scripts")))
                  (install-file "bin/filtlong" bin)
                  (install-file "scripts/histogram.py" scripts)
                  (install-file "scripts/read_info_histograms.sh" scripts))))
            (add-after 'install 'wrap-program
              (lambda _
                (let ((path (getenv "GUIX_PYTHONPATH")))
                  (wrap-program (string-append #$output
                                               "/share/filtlong/scripts/histogram.py")
                    `("GUIX_PYTHONPATH" ":" prefix (,path))))))
            (add-before 'check 'patch-tests
              (lambda _
                (substitute* "scripts/read_info_histograms.sh"
                  (("awk") (which "gawk"))))))))
      (inputs
       (list bash-minimal
             gawk                     ;for read_info_histograms.sh
             python-wrapper           ;required for histogram.py
             zlib))
      (home-page "https://github.com/rrwick/Filtlong/")
      (synopsis "Tool for quality filtering of Nanopore and PacBio data")
      (description
       "The Filtlong package is a tool for filtering long reads by quality.
It can take a set of long reads and produce a smaller, better subset.  It uses
both read length (longer is better) and read identity (higher is better) when
choosing which reads pass the filter.")
      (license (list license:gpl3       ;filtlong
                     license:asl2.0))))) ;histogram.py

(define-public nanopolish
  (package
    (name "nanopolish")
    (version "0.14.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/jts/nanopolish")
             (commit (string-append "v" version))
             (recursive? #t)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1ha9v5ia0qrwgav0956cfc7n64wjm9a9w3rvkg21g37a994yixg5"))
       (modules '((guix build utils)))
       (snippet
        ;; TODO: unbundle slow5lib
        '(begin (for-each delete-file-recursively
                          '("htslib" "minimap2"))))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:make-flags
      #~(list "HDF5=noinstall"
              "EIGEN=noinstall"
              "HTS=noinstall"
              "MINIMAP2=noinstall"
              (string-append "CC=" #$(cc-for-target)))
      #:tests? #f                    ; no check target
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'find-eigen
            (lambda* (#:key inputs #:allow-other-keys)
              (setenv "CPATH"
                      (string-append
                       (search-input-directory inputs "/include/eigen3")
                       ":" (or (getenv "CPATH") "")))))
          (delete 'configure)
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin"))
                    (scripts (string-append #$output "/share/nanopolish/scripts")))

                (install-file "nanopolish" bin)
                (for-each (lambda (file) (install-file file scripts))
                          (find-files "scripts" ".*")))))
          (add-after 'install 'wrap-programs
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((pythonpath (getenv "GUIX_PYTHONPATH"))
                    (perl5lib (getenv "PERL5LIB"))
                    (scripts (string-append #$output "/share/nanopolish/scripts"))
                    (guile (search-input-file inputs "bin/guile")))
                (for-each (lambda (file)
                            (wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))
                          (find-files scripts "\\.py"))
                (for-each (lambda (file)
                            (wrap-script file #:guile guile
                                         `("PERL5LIB" ":" prefix (,perl5lib))))
                          (find-files scripts "\\.pl"))))))))
    (inputs
     (list bash-minimal
           guile-3.0                    ;for wrappers
           eigen
           hdf5
           htslib
           minimap2
           perl
           bioperl-minimal
           perl-getopt-long
           python-wrapper
           python-biopython
           python-numpy
           python-pysam
           python-scikit-learn
           python-scipy
           zlib))
    (native-inputs (list cmake-minimal))
    (home-page "https://github.com/jts/nanopolish")
    (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
    (description
     "This package analyses the Oxford Nanopore sequencing data at signal-level.
Nanopolish can calculate an improved consensus sequence for a draft genome
assembly, detect base modifications, call SNPs (Single nucleotide
polymorphisms) and indels with respect to a reference genome and more.")
    (license license:expat)))

(define-public cnvkit
  (package
    (name "cnvkit")
    (version "0.9.10")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/etal/cnvkit")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0r303pqjg70zpxa564bavbfj99c6di0dafgqqwx2vh4vfsiif94q"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list python-biopython
           python-future
           python-matplotlib
           python-numpy
           python-pandas
           python-pomegranate
           python-pyfaidx
           python-pysam
           python-reportlab
           python-scikit-learn
           python-scipy
           ;; R packages
           r-dnacopy))
    (inputs (list r-minimal)) ;for tests
    (home-page "https://cnvkit.readthedocs.org/")
    (synopsis "Copy number variant detection from targeted DNA sequencing")
    (description
     "CNVkit is a Python library and command-line software toolkit to infer
and visualize copy number from high-throughput DNA sequencing data.  It is
designed for use with hybrid capture, including both whole-exome and custom
target panels, and short-read sequencing platforms such as Illumina and Ion
Torrent.")
    (license license:asl2.0)))

(define-public python-pyfit-sne
  (package
    (name "python-pyfit-sne")
    (version "1.2.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/KlugerLab/pyFIt-SNE")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0f3n7wcmxbnqiisgimhpa6p5chqpb1hj69i6rpg2hv2671i8nn68"))))
    (build-system python-build-system)
    (arguments '(#:tests? #false)) ; there are none
    (propagated-inputs
     (list python-numpy))
    (inputs
     (list fftw))
    (native-inputs
     (list python-cython))
    (home-page "https://github.com/KlugerLab/pyFIt-SNE")
    (synopsis "FFT-accelerated Interpolation-based t-SNE")
    (description
     "t-Stochastic Neighborhood Embedding (t-SNE) is a highly successful
method for dimensionality reduction and visualization of high dimensional
datasets.  A popular implementation of t-SNE uses the Barnes-Hut algorithm to
approximate the gradient at each iteration of gradient descent.  This package
is a Cython wrapper for FIt-SNE.")
    (license license:bsd-4)))

(define-public bbmap
  (package
    (name "bbmap")
    (version "39.01")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sourceforge/bbmap/BBMap_" version ".tar.gz"))
              (sha256
               (base32
                "1rlkw2mlkn699dk9n5lnigmvwq3zr2f8hnq9plx7zi1h06jqsq4q"))))
    (build-system ant-build-system)
    (arguments
     (list
      #:build-target "dist"
      #:tests? #f ; there are none
      #:make-flags
      #~(list (string-append "-Dmpijar="
                             #$(this-package-input "java-openmpi")
                             "/lib/mpi.jar"))
      #:modules '((guix build ant-build-system)
                  (guix build utils)
                  (guix build java-utils))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'build 'build-jni-library
            (lambda _
              (with-directory-excursion "jni"
                (invoke "make" "-f" "makefile.linux"))))
          ;; There is no install target
          (replace 'install (install-jars "dist"))
          (add-after 'install 'install-scripts-and-documentation
            (lambda _
              (substitute* "calcmem.sh"
                (("\\| awk ") (string-append "| " (which "awk") " ")))
              (let* ((scripts (find-files "." "\\.sh$"))
                     (bin (string-append #$output "/bin"))
                     (doc (string-append #$output "/share/doc/bbmap"))
                     (jni (string-append #$output "/lib/jni")))
                (substitute* scripts
                  (("\\$DIR\"\"docs") doc)
                  (("^CP=.*")
                   (string-append "CP=" #$output "/share/java/BBTools.jar\n"))
                  (("^NATIVELIBDIR.*")
                   (string-append "NATIVELIBDIR=" jni "\n"))
                  (("CMD=\"java")
                   (string-append "CMD=\"" (which "java"))))
                (for-each (lambda (script) (install-file script bin)) scripts)

                ;; Install JNI library
                (install-file "jni/libbbtoolsjni.so" jni)

                ;; Install documentation
                (install-file "docs/readme.txt" doc)
                (copy-recursively "docs/guides" doc)))))
       #:jdk openjdk11))
    (inputs
     (list gawk java-eclipse-jdt-core java-eclipse-jdt-compiler-apt
           java-openmpi))
    (home-page "https://sourceforge.net/projects/bbmap/")
    (synopsis "Aligner and other tools for short sequencing reads")
    (description
     "This package provides bioinformatic tools to align, deduplicate,
reformat, filter and normalize DNA and RNA-seq data.  It includes the
following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm,
a kmer-based error-correction and normalization tool; Dedupe, a tool to
simplify assemblies by removing duplicate or contained subsequences that share
a target percent identity; Reformat, to convert reads between
fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over
500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches
to an artifact/contaminant file.")
    (license license:bsd-3)))

(define-public velvet
  (package
    (name "velvet")
    (version "1.2.10")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.ebi.ac.uk/~zerbino/velvet/"
                                  "velvet_" version ".tgz"))
              (sha256
               (base32
                "0h3njwy66p6bx14r3ar1byb0ccaxmxka4c65rn4iybyiqa4d8kc8"))
              ;; Delete bundled libraries
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (delete-file "Manual.pdf")
                  (delete-file-recursively "third-party")))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:make-flags #~(list "OPENMP=t")
      #:test-target "test"
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (add-after 'unpack 'fix-zlib-include
            (lambda _
              (substitute* "src/binarySequences.c"
                (("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))))
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin"))
                    (doc (string-append #$output "/share/doc/velvet")))
                (mkdir-p bin)
                (mkdir-p doc)
                (install-file "velveth" bin)
                (install-file "velvetg" bin)
                (install-file "Manual.pdf" doc)
                (install-file "Columbus_manual.pdf" doc)))))))
    (inputs
     (list openmpi zlib))
    (native-inputs
     (list (texlive-updmap.cfg
            (list texlive-infwarerr
                  texlive-kvoptions
                  texlive-pdftexcmds))))
    (home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
    (synopsis "Nucleic acid sequence assembler for very short reads")
    (description
     "Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454.  Velvet currently takes in
short read sequences, removes errors then produces high quality unique
contigs.  It then uses paired read information, if available, to retrieve the
repeated areas between contigs.")
    (license license:gpl2+)))

(define-public vembrane
  (package
    (name "vembrane")
    (version "0.13.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/vembrane/vembrane")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1gdih56gpqd8ks3sd4ah844kac09hi3g073k9gvazb32ah50900w"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "pyproject.toml"
               (("pysam = \"\\^0.19\"") "pysam = \"^0.20\"")
               (("numpy = \\{ version = \"\\^1.23\"")
                "numpy = { version = \"^1\"")))))))
    (inputs
     (list python-asttokens python-intervaltree python-numpy
           python-pysam python-pyyaml))
    (native-inputs
     (list poetry python-pytest))
    (home-page "https://github.com/vembrane/vembrane")
    (synopsis "Filter VCF/BCF files with Python expressions.")
    (description "Vembrane simultaneously filters variants based on
any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the
annotation field ANN.  When filtering based on ANN, annotation entries are
filtered first.  If no annotation entry remains, the entire variant is
deleted.")
    (license license:expat)))

(define-public python-velocyto
  (package
    (name "python-velocyto")
    (version "0.17.17")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "velocyto" version))
       (sha256
        (base32
         "0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs"))
       (modules '((guix build utils)))
       ;; Delete generated C files.
       (snippet
        '(for-each delete-file (find-files "." "\\.c")))))
    (build-system python-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         ;; Numba needs a writable dir to cache functions.
         (add-before 'check 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (native-inputs
     (list python-joblib))
    (propagated-inputs
     (list python-click
           python-cython
           python-h5py
           python-loompy
           python-matplotlib
           python-numba
           python-numpy
           python-pandas
           python-pysam
           python-scikit-learn
           python-scipy))
    (home-page "https://github.com/velocyto-team/velocyto.py")
    (synopsis "RNA velocity analysis for single cell RNA-seq data")
    (description
     "Velocyto is a library for the analysis of RNA velocity.  Velocyto
includes a command line tool and an analysis pipeline.")
    (license license:bsd-2)))

(define-public arriba
  (package
    (name "arriba")
    (version "1.0.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/suhrig/arriba/releases/"
                           "download/v" version "/arriba_v" version ".tar.gz"))
       (sha256
        (base32
         "0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (replace 'configure
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "Makefile"
                (("-I\\$\\(HTSLIB\\)/htslib")
                 (string-append "-I"
                                (search-input-directory inputs "/include/htslib")))
                ((" \\$\\(HTSLIB\\)/libhts.a")
                 (string-append " " (search-input-file inputs "/lib/libhts.so"))))
              (let ((samtools (search-input-file inputs "/bin/samtools")))
                (substitute* "run_arriba.sh"
                  (("^STAR ")
                   (string-append (search-input-file inputs "/bin/STAR") " "))
                  (("samtools --version-only")
                   (string-append samtools " --version-only"))
                  (("samtools index")
                   (string-append samtools " index"))
                  (("samtools sort")
                   (string-append samtools " sort"))))))
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin")))
                (install-file "arriba" bin)
                (install-file "run_arriba.sh" bin)
                (install-file "draw_fusions.R" bin)
                (wrap-program (string-append bin "/draw_fusions.R")
                  `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))))))))
    (inputs
     (list bash-minimal
           htslib
           r-minimal
           r-circlize
           r-genomicalignments
           r-genomicranges
           samtools
           star
           zlib))
    (home-page "https://github.com/suhrig/arriba")
    (synopsis "Gene fusion detection from RNA-Seq data")
    (description
     "Arriba is a command-line tool for the detection of gene fusions from
RNA-Seq data.  It was developed for the use in a clinical research setting.
Therefore, short runtimes and high sensitivity were important design criteria.
It is based on the fast STAR aligner and the post-alignment runtime is
typically just around two minutes.  In contrast to many other fusion detection
tools which build on STAR, Arriba does not require to reduce the
@code{alignIntronMax} parameter of STAR to detect small deletions.")
    ;; All code is under the Expat license with the exception of
    ;; "draw_fusions.R", which is under GPLv3.
    (license (list license:expat license:gpl3))))

(define-public adapterremoval
  (package
    (name "adapterremoval")
    (version "2.3.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/MikkelSchubert/adapterremoval")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0wyr182667wqdmzhwwa6f7dddr8kk0scgzb8lsm23wim544mvn6i"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:make-flags
      #~(list "COLOR_BUILD=no"
              (string-append "PREFIX=" #$output))
      #:test-target "test"
      #:phases
      '(modify-phases %standard-phases
         (delete 'configure))))
    (inputs (list zlib))
    (home-page "https://adapterremoval.readthedocs.io/")
    (synopsis "Rapid sequence adapter trimming, identification, and read merging")
    (description
     "This program searches for and removes remnant adapter sequences from
@dfn{High-Throughput Sequencing} (HTS) data and (optionally) trims low quality
bases from the 3' end of reads following adapter removal.  AdapterRemoval can
analyze both single end and paired end data, and can be used to merge
overlapping paired-ended reads into (longer) consensus sequences.
Additionally, the AdapterRemoval may be used to recover a consensus adapter
sequence for paired-ended data, for which this information is not available.")
    (license license:gpl3+)))

(define-public checkm
  (package
    (name "checkm")
    (version "1.1.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "checkm-genome" version))
       (sha256
        (base32
         "0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz"))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #f ; Some tests fail for unknown reasons.
       #:phases
       (modify-phases %standard-phases
         (add-before 'check 'set-HOME
           (lambda _
             (setenv "HOME" "/tmp"))))))
    (inputs
     (list python-dendropy python-matplotlib python-numpy python-pysam
           python-scipy))
    (home-page "https://ecogenomics.github.io/CheckM/")
    (synopsis "Assess the quality of putative genome bins")
    (description
     "CheckM provides a set of tools for assessing the quality of genomes
recovered from isolates, single cells, or metagenomes.  It provides robust
estimates of genome completeness and contamination by using collocated sets of
genes that are ubiquitous and single-copy within a phylogenetic lineage.
Assessment of genome quality can also be examined using plots depicting key
genomic characteristics (e.g., GC, coding density) which highlight sequences
outside the expected distributions of a typical genome.  CheckM also provides
tools for identifying genome bins that are likely candidates for merging based
on marker set compatibility, similarity in genomic characteristics, and
proximity within a reference genome.")
    (license license:gpl3+)))

(define-public umi-tools
  (package
    (name "umi-tools")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "umi_tools" version))
       (sha256
        (base32
         "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
    (build-system python-build-system)
    (inputs
     (list python-pandas
           python-future
           python-scipy
           python-matplotlib
           python-regex
           python-pysam))
    (native-inputs
     (list python-cython))
    (home-page "https://github.com/CGATOxford/UMI-tools")
    (synopsis "Tools for analyzing unique modular identifiers")
    (description "This package provides tools for dealing with @dfn{Unique
Molecular Identifiers} (UMIs) and @dfn{Random Molecular Tags} (RMTs) in
genetic sequences.  There are six tools: the @code{extract} and
@code{whitelist} commands are used to prepare a fastq containing UMIs @code{+/-}
cell barcodes for alignment.  The remaining commands, @code{group},
@code{dedup}, and @{count}/@code{count_tab}, are used to identify PCR
duplicates using the UMIs and perform different levels of analysis depending
on the needs of the user.")
    (license license:expat)))

(define-public ataqv
  (package
    (name "ataqv")
    (version "1.0.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/ParkerLab/ataqv")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "031xr6jx1aprh26y5b1lv3gzrlmzg4alfl73vvshymx8cq8asrqi"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       ,#~(list (string-append "prefix=" #$output)
                (string-append "BOOST_ROOT="
                               #$(this-package-input "boost"))
                (string-append "HTSLIB_ROOT="
                               #$(this-package-input "htslib")))
       #:test-target "test"
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (inputs
     (list boost htslib ncurses zlib))
    (native-inputs
     (list lcov))
    (home-page "https://github.com/ParkerLab/ataqv")
    (synopsis "Toolkit for quality control and visualization of ATAC-seq data")
    (description "This package provides a toolkit for measuring and comparing
ATAC-seq results.  It was written to make it easier to spot differences that
might be caused by ATAC-seq library prep or sequencing.  The main program,
@code{ataqv}, examines aligned reads and reports some basic metrics.")
    (license license:gpl3+)))

(define-public r-psiplot
  (package
    (name "r-psiplot")
    (version "2.3.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/kcha/psiplot")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-mass
           r-dplyr
           r-tidyr
           r-purrr
           r-readr
           r-magrittr
           r-ggplot2))
    (home-page "https://github.com/kcha/psiplot")
    (synopsis "Plot percent spliced-in values of alternatively-spliced exons")
    (description
     "PSIplot is an R package for generating plots of @dfn{percent
spliced-in} (PSI) values of alternatively-spliced exons that were computed by
vast-tools, an RNA-Seq pipeline for alternative splicing analysis.  The plots
are generated using @code{ggplot2}.")
    (license license:expat)))

(define-public r-scopeloomr
  (let ((commit "99726f5f7da794042036b73924b6a10d6e7b4d5d")
        (revision "1"))
    (package
      (name "r-scopeloomr")
      (version (git-version "0.13.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/aertslab/SCopeLoomR")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1ci17ms0c0hf7yfp9ckcg7a2y1s0nm19jj3cifsd55hwc0gdglmz"))))
      (properties `((upstream-name . "SCopeLoomR")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-base64enc r-hdf5r r-igraph r-matrix r-plyr r-rjson r-rlist))
      (home-page "https://github.com/aertslab/SCopeLoomR")
      (synopsis "Build .loom files and extract data from them")
      (description
       "This is an R package to build generic @code{.loom} files aligning with
the default naming convention of the @code{.loom} format and to integrate
other data types e.g.: regulons (SCENIC), clusters from Seurat, trajectory
information...  The package can also be used to extract data from @code{.loom}
files.")
      (license license:expat))))

(define-public rscape
  (package
    (name "rscape")
    (version "2.0.0.q")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://eddylab.org/software/rscape/"
                                  "rscape_v" version ".tar.gz"))
              (sha256
               (base32
                "1jabvm3fzh8iy4803ns12v1fsy28x6wdy8wx4ik8y0mfac4h787q"))))
    (build-system gnu-build-system)
    (propagated-inputs (list gsl openmpi))
    (native-inputs (list automake autoconf))
    (home-page "https://github.com/EddyRivasLab/R-scape")
    (synopsis "RNA structural covariation above phylogenetic expectation")
    (description
     "R-scape discovers RNA secondary structure consensus elements.
These elements include riboswitches and ribozymes.  It utilizes probabilistic
modeling of sequence alignments, explicitly considering folding dependencies.
The tool enables the de novo search for new structural elements and
facilitates comparative analysis of known RNA families.")
    (license license:bsd-3)))

(define-public r-databaselinke-r
  (let ((commit "cf3d6cc3d36f2e1c9a557390232e9a8ed5abb7fd")
        (revision "1"))
    (package
      (name "r-databaselinke-r")
      (version (git-version "1.7.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/vertesy/DatabaseLinke.R")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0hk76sb3w1v8a7c1knpc572ypsbgqlrv0p49c9y55a0dr12n16s1"))))
      (properties `((upstream-name . "DatabaseLinke.R")))
      (build-system r-build-system)
      (propagated-inputs (list r-readwriter))
      (home-page "https://github.com/vertesy/DatabaseLinke.R")
      (synopsis
       "Parse links to databases from your list of gene symbols")
      (description
       "This package provides a set of functions to parse and open (search
query) links to genomics related and other websites for R.  Useful when you
want to explore e.g.: the function of a set of differentially expressed
genes.")
      (license license:gpl3))))

(define-public r-seurat-utils
  (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
        (revision "1"))
    (package
      (name "r-seurat-utils")
      (version (git-version "2.5.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/vertesy/Seurat.utils")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
      (properties `((upstream-name . "Seurat.utils")))
      (build-system r-build-system)
      (propagated-inputs (list r-codeandroll2
                               r-cowplot
                               r-databaselinke-r
                               r-dplyr
                               r-enhancedvolcano
                               r-foreach
                               r-ggcorrplot
                               r-ggexpress
                               r-ggplot2
                               r-ggpubr
                               r-ggrepel
                               r-hgnchelper
                               r-htmlwidgets
                               r-job
                               r-magrittr
                               r-markdownhelpers
                               r-markdownreports
                               r-matrix
                               r-matrixstats
                               r-pheatmap
                               r-plotly
                               r-princurve
                               r-qs
                               r-r-utils
                               r-readr
                               r-readwriter
                               r-reshape2
                               r-rstudioapi
                               r-scales
                               r-seurat
                               r-soupx
                               r-sparsematrixstats
                               r-stringendo
                               r-stringr
                               r-tibble
                               r-tictoc
                               r-tidyverse
                               r-vroom))
      (home-page "https://github.com/vertesy/Seurat.utils")
      (synopsis "Collection of utility functions for Seurat")
      (description
       "This is a collection of utility functions for Seurat.  These functions
allow the automation and multiplexing of plotting, 3D plotting, visualization
of statistics & QC, interaction with the Seurat object.  Some functionalities
require functions from CodeAndRoll and MarkdownReports libraries.")
      (license license:gpl3))))

(define-public r-seuratextend
  (let ((commit "5382e921f7b365c7b75b20d07cb455e4390fe36f")
        (revision "1"))
    (package
      (name "r-seuratextend")
      (version (git-version "1.0.7" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/huayc09/SeuratExtend")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1rlx20jyfdrymxn8b9dsf9n9jk9rwjjx1wy2f00layvd57g9ch2q"))))
      (properties `((upstream-name . "SeuratExtend")))
      (build-system r-build-system)
      (propagated-inputs (list r-biocmanager
                               r-dplyr
                               r-ggplot2
                               r-ggpubr
                               r-glue
                               r-hdf5r
                               r-magrittr
                               r-mosaic
                               r-purrr
                               r-remotes
                               r-reshape2
                               r-reticulate
                               r-rlist
                               r-scales
                               r-seurat
                               r-seuratextenddata
                               r-seuratobject
                               r-tidyr))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/huayc09/SeuratExtend")
      (synopsis "Enhanced toolkit for scRNA-seq analysis")
      (description
       "This package is designed to improve and simplify the analysis of
scRNA-seq data.  It uses the Seurat object for this purpose.  It provides an
array of enhanced visualization tools, an integrated functional and pathway
analysis pipeline, seamless integration with popular Python tools, and a suite
of utility functions to aid in data manipulation and presentation.")
      (license license:gpl3+))))

(define-public r-seuratextenddata
  (let ((commit "e7f17d4bacca436705b06b2cd0c879f83add9271")
        (revision "1"))
    (package
      (name "r-seuratextenddata")
      (version (git-version "0.2.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/huayc09/SeuratExtendData")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "1vl2wvpbv5q04mzc6z3f1jw2jc5i8pw5vm8y1rg5b1cihkwppvq5"))))
      (properties `((upstream-name . "SeuratExtendData")))
      (build-system r-build-system)
      (home-page "https://github.com/huayc09/SeuratExtendData")
      (synopsis "Data attached to SeuratExtend package")
      (description "This package provides data for the SeuratExtend tool.")
      (license license:gpl3+))))

(define-public r-seuratwrappers
  ;; There are no releases or tags.
  (let ((commit "d28512f804d5fe05e6d68900ca9221020d52cf1d")
        (revision "1"))
    (package
      (name "r-seuratwrappers")
      (version (git-version "0.3.1" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/satijalab/seurat-wrappers")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0rm74y2fj3cmiqn7jz1ald8jbw53c2qxkj3mgl4pxih9vx39jhgy"))))
      (properties `((upstream-name . "SeuratWrappers")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biocmanager
             r-cowplot
             r-ggplot2
             r-igraph
             r-matrix
             r-remotes
             r-rlang
             r-rsvd
             r-r-utils
             r-seurat))
      (home-page "https://github.com/satijalab/seurat-wrappers")
      (synopsis "Community-provided methods and extensions for the Seurat object")
      (description
       "SeuratWrappers is a collection of community-provided methods and
extensions for Seurat, curated by the Satija Lab at NYGC.  These methods
comprise functionality not presently found in Seurat, and are able to be
updated much more frequently.")
      (license license:gpl3))))

(define-public python-ctxcore
  (package
    (name "python-ctxcore")
    (version "0.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/aertslab/ctxcore")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0nv4lc46cnzpg5gcdxrsv7b4srmkq55zl3rcadw5pn3yyz5fzd2k"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'build 'pretend-version
            ;; The version string is usually derived via setuptools-scm, but
            ;; it doesn't work without the .git directory.
            (lambda _
              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
    (propagated-inputs
     (list python-cytoolz
           python-frozendict
           python-numba
           python-numpy
           python-pandas
           python-pyarrow
           python-pyyaml
           python-tqdm))
    (native-inputs
     (list python-pytest
           python-setuptools-scm))
    (home-page "https://github.com/aertslab/ctxcore")
    (synopsis "Core functions for pycisTarget and the SCENIC tool suite")
    (description
     "ctxcore is part of the SCENIC suite of tools.  It provides core functions for
pycisTarget and SCENIC.")
    (license license:gpl3+)))

(define-public python-arboreto
  (package
    (name "python-arboreto")
    (version "0.1.6")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/aertslab/arboreto")
                    (commit "2f475dca08f47a60acc2beb8dd897e77b7495ca4")))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0l0im8ay7l2d24f7vaha454vsaha9s36bfqhbijg3b8ir8apsd7l"))))
    (build-system python-build-system)
    ;; Lots of tests fail because python-distributed fails to start the
    ;; "Nanny" process.
    (arguments '(#:tests? #false))
    (propagated-inputs
     (list python-bokeh
           python-dask
           python-distributed
           python-lz4
           python-numpy
           python-pandas
           python-pyarrow
           python-scikit-learn
           python-scipy
           python-tornado-6))
    (home-page "https://github.com/aertslab/arboreto")
    (synopsis "Gene regulatory network inference using tree-based ensemble regressors")
    (description
     "This package implements scalable gene regulatory network inference using
tree-based ensemble regressors.")
    (license license:bsd-3)))

(define-public pyscenic
  ;; Latest commit from the update-pyarrow branch
  (let ((commit "5f170fdf474548c37ab381d1849c662820d658ee")
        (revision "1"))
    (package
      (name "pyscenic")
      (version (git-version "0.11.2" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/aertslab/pySCENIC")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "03qkvy400rjndg2ds6bhcaprir71mqr2v3yv9vd77lcnzxgw3s0z"))))
      (build-system pyproject-build-system)
      (arguments
       (list
        #:phases
        '(modify-phases %standard-phases
           ;; The cli modules referenced here have been removed, so this
           ;; breaks the sanity check.
           (add-after 'unpack 'do-not-reference-deleted-modules
             (lambda _
               (substitute* "setup.py"
                 (("'db2feather = .*',") "")
                 (("'invertdb = .*',") "")
                 (("'gmt2regions = pyscenic.cli.gmt2regions:main'") ""))))
           ;; Numba needs a writable dir to cache functions.
           (add-before 'check 'set-numba-cache-dir
             (lambda _
               (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
      (propagated-inputs
       (list python-ctxcore
             python-cytoolz
             python-multiprocessing-on-dill
             python-llvmlite
             python-numba
             python-attrs
             python-frozendict
             python-numpy
             python-pandas
             python-cloudpickle
             python-dask
             python-pyarrow               ;XXX for dask
             python-distributed
             python-arboreto
             python-boltons
             python-setuptools
             python-pyyaml
             python-tqdm
             python-interlap
             python-umap-learn
             python-loompy
             python-networkx
             python-scipy
             python-fsspec
             python-requests
             python-aiohttp
             python-scikit-learn))
      (native-inputs
       (list python-pytest))
      (home-page "https://scenic.aertslab.org/")
      (synopsis "Single-Cell regulatory network inference and clustering")
      (description
       "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell
rEgulatory Network Inference and Clustering) which enables biologists to infer
transcription factors, gene regulatory networks and cell types from
single-cell RNA-seq data.")
      (license license:gpl3+))))

(define-public python-ikarus
  (package
    (name "python-ikarus")
    (version "0.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "ikarus" version))
       (sha256
        (base32
         "086czpvj4yafz4vrq5rx2gy0bj2l8nzwnkk0gw8qvy4w133xjysy"))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #false
       #:phases
       (modify-phases %standard-phases
         ;; See https://github.com/BIMSBbioinfo/ikarus/issues/12
         (add-after 'unpack 'fix-issue-12
           (lambda _
             (substitute* "ikarus/classifier.py"
               (("pyscenic.genesig") "ctxcore.genesig"))))
         ;; Numba needs a writable dir to cache functions.
         (add-before 'check 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
    (propagated-inputs
     (list python-numpy
           python-pandas
           python-scipy
           python-scanpy
           python-anndata
           python-ctxcore ;because of issue 12
           pyscenic))
    (home-page "https://github.com/BIMSBbioinfo/ikarus")
    (synopsis "Machine learning classifier of tumor cells")
    (description
     "ikarus is a stepwise machine learning pipeline that tries to cope with a task
of distinguishing tumor cells from normal cells.  Leveraging multiple
annotated single cell datasets it can be used to define a gene set specific to
tumor cells.  First, the latter gene set is used to rank cells and then to
train a logistic classifier for the robust classification of tumor and normal
cells.  Finally, sensitivity is increased by propagating the cell labels based
on a custom cell-cell network.  ikarus is tested on multiple single cell
datasets to ascertain that it achieves high sensitivity and specificity in
multiple experimental contexts.")
    (license license:expat)))

(define-public vbz-compression
  (package
    (name "vbz-compression")
    (version "1.0.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/nanoporetech/vbz_compression/")
             (commit (string-append "v" version))
             ;; We include the streamvbyte sources
             (recursive? #true)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1rn5d98flvjblhj4zjpcdqqh8qlgsh5cmb13i49fnm187p03097z"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       '("-DENABLE_CONAN=OFF"
         ;; Python things aren't even installed, so we might as well
         ;; disable building them.
         "-DENABLE_PYTHON=OFF")))
    (inputs
     (list ;("hdf5" ,hdf5-1.10)
           `(,zstd "lib")))
    (native-inputs
     (list googlebenchmark))
    (home-page "https://github.com/nanoporetech/vbz_compression/")
    (synopsis "VBZ compression plugin for nanopore signal data")
    (description
     "VBZ Compression uses variable byte integer encoding to compress
nanopore signal data.  The performance of VBZ is achieved by taking
advantage of the properties of the raw signal and therefore is most
effective when applied to the signal dataset.")
    (license license:mpl2.0)))

(define-public python-ont-fast5-api
  (package
    (name "python-ont-fast5-api")
    (version "4.0.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/nanoporetech/ont_fast5_api")
             (commit (string-append "release_" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "01hj4751j424lzic2sc4bz1f8w7i7fpkjpy3rgghdyl5lyfyb4s4"))
       (modules '((guix build utils)))
       (snippet
        '(delete-file-recursively "ont_fast5_api/vbz_plugin"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'copy-plugin
           (lambda* (#:key inputs #:allow-other-keys)
             (mkdir-p "ont_fast5_api/vbz_plugin/")
             (install-file (string-append
                            (assoc-ref inputs "vbz-compression")
                            "/hdf5/lib/plugin/libvbz_hdf_plugin.so")
                           "ont_fast5_api/vbz_plugin/"))))))
    (inputs
     (list vbz-compression))
    (propagated-inputs
     (list python-numpy python-h5py python-packaging python-progressbar33))
    (home-page "https://github.com/nanoporetech/ont_fast5_api")
    (synopsis "Interface to HDF5 files of the Oxford Nanopore fast5 file format")
    (description
     "This package provides a concrete implementation of the fast5 file schema
using the generic @code{h5py} library, plain-named methods to interact with
and reflect the fast5 file schema, and tools to convert between
@code{multi_read} and @code{single_read} formats.")
    (license license:mpl2.0)))

(define-public tbsp
  (let ((commit "dc30c03868233c5504299c9cb0d7b2064ba9cb41")
        (revision "2"))
    (package
      (name "tbsp")
      (version (git-version "1.0.0" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/phoenixding/tbsp")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "1im0bik2hxkcb7jzkcxp5nqb30hd8lfraxml6i5ik52j6z3qqln1"))))
      (build-system python-build-system)
      (arguments
       '(#:tests? #f         ; no tests included
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
               (substitute* "setup.py"
                 ((", <3.0") ""))))))) ; matplotlib
      (inputs
       (list python-matplotlib
             python-networkx
             python-numpy
             python-pybigwig
             python-biopython-1.73
             python-scikit-learn
             python-scipy))
      (home-page "https://github.com/phoenixding/tbsp/")
      (synopsis "SNP-based trajectory inference")
      (description
       "Several studies focus on the inference of developmental and response
trajectories from single cell RNA-Seq (scRNA-Seq) data.  A number of
computational methods, often referred to as pseudo-time ordering, have been
developed for this task.  CRISPR has also been used to reconstruct lineage
trees by inserting random mutations.  The tbsp package implements an
alternative method to detect significant, cell type specific sequence
mutations from scRNA-Seq data.")
      (license license:expat))))

(define-public tabixpp
  (package
   (name "tabixpp")
   (version "1.1.2")
   (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/ekg/tabixpp")
                   (commit (string-append "v" version))))
             (file-name (git-file-name name version))
             (sha256
              (base32 "00aqs147yn8zcvxims5njwxqsbnlbjv7lnmiwqy80bfdcbhljkqf"))
             (modules '((guix build utils)))
             (snippet
              '(delete-file-recursively "htslib"))))
   (build-system gnu-build-system)
   (inputs
    (list bzip2 curl htslib xz zlib))
   (arguments
    (list #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
                               (string-append "CXX=" #$(cxx-for-target))
                               "HTS_HEADERS="
                               (string-append "HTS_LIB="
                                              (search-input-file %build-inputs
                                                                 "/lib/libhts.a"))
                               "INCLUDES=")
          #:tests? #f ; There are no tests to run.
          #:phases
          #~(modify-phases %standard-phases
              (delete 'configure) ; There is no configure phase.
              ;; Build shared and static libraries.
              (add-after 'build 'build-libraries
                (lambda* (#:key inputs #:allow-other-keys)
                  (invoke #$(cxx-for-target)
                          "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts")
                  (invoke #$(ar-for-target) "rcs" "libtabixpp.a" "tabix.o")))
              (replace 'install
                (lambda _
                  (let ((lib (string-append #$output "/lib"))
                        (bin (string-append #$output "/bin")))
                    (install-file "tabix++" bin)
                    (install-file "libtabixpp.so" lib)
                    (install-file "libtabixpp.a" lib)
                    (install-file "tabix.hpp" (string-append #$output "/include"))
                    (mkdir-p (string-append lib "/pkgconfig"))
                    (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc")
                      (lambda _
                        (format #t "\
prefix=~a~@
exec_prefix=${prefix}~@
libdir=${exec_prefix}/lib~@
includedir=${prefix}/include~@
~@
~@
Name: libtabixpp~@
Version: ~a~@
Description: C++ wrapper around tabix project~@
Libs: -L${libdir} -ltabixpp~@
Cflags: -I${includedir}~%"
                                #$output #$version)))))))))
   (home-page "https://github.com/ekg/tabixpp")
   (synopsis "C++ wrapper around tabix project")
   (description "This is a C++ wrapper around the Tabix project which abstracts
some of the details of opening and jumping in tabix-indexed files.")
   (license license:expat)))

(define-public smithwaterman
  (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7"))
    (package
      (name "smithwaterman")
      (version (git-version "0.0.0" "2" commit))
      (source (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/ekg/smithwaterman/")
              (commit commit)))
        (file-name (git-file-name name version))
        (sha256
         (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs"))))
      (build-system gnu-build-system)
      (arguments
       (list
         #:tests? #f ; There are no tests to run.
         #:make-flags
         #~(list (string-append "CXX=" #$(cxx-for-target))
                 "libsw.a" "all")
         #:phases
         #~(modify-phases %standard-phases
             (delete 'configure) ; There is no configure phase.
             (add-after 'unpack 'patch-source
               (lambda _
                 (substitute* "Makefile"
                   (("-c ") "-c -fPIC "))
                 #$@(if (%current-target-system)
                     #~((substitute* "Makefile"
                          (("\tld")
                           (string-append "\t" #$(%current-target-system) "-ld"))
                          (("\tar")
                           (string-append "\t" #$(%current-target-system) "-ar"))))
                     '())))
             (add-after 'build 'build-dynamic
               (lambda _
                 (invoke #$(cxx-for-target)
                         "-shared" "-o" "libsmithwaterman.so"
                         "smithwaterman.o" "SmithWatermanGotoh.o"
                         "disorder.o" "BandedSmithWaterman.o"
                         "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
             (replace 'install
               (lambda* (#:key outputs #:allow-other-keys)
                 (let* ((out (assoc-ref outputs "out"))
                        (bin (string-append out "/bin"))
                        (lib (string-append out "/lib")))
                   (install-file "smithwaterman" bin)
                   (for-each
                     (lambda (file)
                       (install-file file (string-append out "/include/smithwaterman")))
                     (find-files "." "\\.h$"))
                   (install-file "libsmithwaterman.so" lib)
                   (install-file "libsw.a" lib)
                   (mkdir-p (string-append lib "/pkgconfig"))
                   (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc")
                     (lambda _
                       (format #t "prefix=~a~@
                               exec_prefix=${prefix}~@
                               libdir=${exec_prefix}/lib~@
                               includedir=${prefix}/include/smithwaterman~@
                               ~@
                               ~@
                               Name: smithwaterman~@
                               Version: ~a~@
                               Description: smith-waterman-gotoh alignment algorithm~@
                               Libs: -L${libdir} -lsmithwaterman~@
                               Cflags: -I${includedir}~%"
                               out #$version)))))))))
      (home-page "https://github.com/ekg/smithwaterman")
      (synopsis "Implementation of the Smith-Waterman algorithm")
      (description "Implementation of the Smith-Waterman algorithm.")
      ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
      (license (list license:gpl2 license:expat)))))

(define-public sylamer
  (package
    (name "sylamer")
    (version "18-131")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/micans/sylamer/")
                    (commit "aa75c3584797c0c15f860addb645f7bc1dd7627d")))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1ddiwlrdghhb4574rvfw0brjp9gs5l6nfsy82h0m4mvz1dr3gkj5"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ; no test target
      #:make-flags
      #~(list (string-append "GSLPREFIX=" #$(this-package-input "gsl")))
      #:phases
      '(modify-phases %standard-phases
         (replace 'configure
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "Makefile"
               (("cp sylamer \\$\\(HOME\\)/local/bin")
                (string-append "install -D -t " (assoc-ref outputs "out")
                               "/bin sylamer")))
             (install-file "Makefile" "src")
             (chdir "src"))))))
    (inputs (list gsl zlib))
    (home-page "https://www.ebi.ac.uk/research/enright/software/sylamer")
    (synopsis "Asses microRNA binding and siRNA off-target effects")
    (description "Sylamer is a system for finding significantly over or
under-represented words in sequences according to a sorted gene list.
Typically it is used to find significant enrichment or depletion of microRNA
or siRNA seed sequences from microarray expression data.  Sylamer is extremely
fast and can be applied to genome-wide datasets with ease.  Results are
plotted in terms of a significance landscape plot.  These plots show
significance profiles for each word studied across the sorted genelist.")
    (license license:gpl3+)))

(define-public multichoose
  (package
    (name "multichoose")
    (version "1.0.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/ekg/multichoose/")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;Tests require node.
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)           ;There is no configure phase.
          (replace 'install
            (lambda _
              (let ((bin (string-append #$output "/bin"))
                    (include (string-append #$output "/include")))
                ;; TODO: There are Python modules for these programs too.
                (install-file "multichoose" bin)
                (install-file "multipermute" bin)
                (install-file "multichoose.h" include)
                (install-file "multipermute.h" include)))))))
    (home-page "https://github.com/ekg/multichoose")
    (synopsis "Efficient loopless multiset combination generation algorithm")
    (description "This library implements an efficient loopless multiset
combination generation algorithm which is (approximately) described in
\"Loopless algorithms for generating permutations, combinations, and other
combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
1973. (Algorithm 7.)")
    (license license:expat)))

(define-public fsom
  (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
    (package
      (name "fsom")
      (version (git-version "0.0.0" "1" commit))
      (source (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/ekg/fsom/")
              (commit commit)))
        (file-name (git-file-name name version))
        (sha256
         (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; There are no tests to run.
         #:phases
         (modify-phases %standard-phases
           (delete 'configure) ; There is no configure phase.
           (replace 'install
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                 (install-file "fsom" bin)))))))
      (native-inputs
       (list gcc-6))
      (home-page "https://github.com/ekg/fsom")
      (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
      (description "A tiny C library for managing SOM (Self-Organizing Maps)
neural networks.")
      (license license:gpl3))))

(define-public fastahack
  (package
    (name "fastahack")
    (version "1.0.0")
    (source (origin
      (method git-fetch)
      (uri (git-reference
            (url "https://github.com/ekg/fastahack/")
            (commit (string-append "v" version))))
      (file-name (git-file-name name version))
      (sha256
       (base32 "0rp1blskhzxf7vbh253ibpxbgl9wwgyzf1wbkxndi08d3j4vcss9"))))
    (build-system gnu-build-system)
    (arguments
     (list #:make-flags #~(list (string-append "CXX=" #$(cxx-for-target)))
           ;; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15
           #:tests? #f
           #:phases
           #~(modify-phases %standard-phases
               (delete 'configure) ; There is no configure phase.
               (add-after 'unpack 'patch-source
                 (lambda _
                   (substitute* "Makefile"
                     (("-c ") "-c -fPIC "))))
               (add-after 'build 'build-dynamic
                 (lambda _
                   (invoke #$(cxx-for-target)
                           "-shared" "-o" "libfastahack.so"
                           "Fasta.o" "FastaHack.o" "split.o" "disorder.o")))
               (replace 'install
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let* ((out (assoc-ref outputs "out"))
                          (lib (string-append out "/lib"))
                          (bin (string-append out "/bin")))
                     (mkdir-p (string-append out "/include/fastahack"))
                     (for-each
                      (lambda (file)
                        (install-file file (string-append out "/include/fastahack")))
                      (find-files "." "\\.h$"))
                     (install-file "fastahack" bin)
                     (install-file "libfastahack.so" lib)
                     (mkdir-p (string-append lib "/pkgconfig"))
                     (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc")
                       (lambda _
                         (format #t "prefix=~a~@
                           exec_prefix=${prefix}~@
                           libdir=${exec_prefix}/lib~@
                           includedir=${prefix}/include/fastahack~@
                           ~@
                           ~@
                           Name: fastahack~@
                           Version: ~a~@
                           Description: Indexing and sequence extraction from FASTA files~@
                           Libs: -L${libdir} -lfastahack~@
                           Cflags: -I${includedir}~%"
                                 out #$version)))))))))
    (home-page "https://github.com/ekg/fastahack")
    (synopsis "Indexing and sequence extraction from FASTA files")
    (description "Fastahack is a small application for indexing and
extracting sequences and subsequences from FASTA files.  The included library
provides a FASTA reader and indexer that can be embedded into applications
which would benefit from directly reading subsequences from FASTA files.  The
library automatically handles index file generation and use.")
    (license (list license:expat license:gpl2))))

(define-public wfa2-lib
  (package
    (name "wfa2-lib")
    (version "2.3.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/smarco/WFA2-lib")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "110s1s79z8ndjs4qdgmrj708iiaqyagia3gi2fxak101lg263diw"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          ;; This pkg-config file is provided by other distributions.
          (add-after 'install 'install-pkg-config-file
            (lambda _
              (let ((pkgconfig (string-append #$output "/lib/pkgconfig")))
                (mkdir-p pkgconfig)
                (with-output-to-file (string-append pkgconfig "/libwfa2.pc")
                  (lambda _
                    (format #t "\
prefix=~a~@
exec_prefix=${prefix}~@
libdir=${exec_prefix}/lib~@
includedir=${prefix}/include/wfa2lib~@
~@
Name: libwfa2~@
Version: ~a~@
Description: Wavefront alignment algorithm library~@
Libs: -L${libdir} -lwfa2 -lwfa2cpp~@
Cflags: -I${includedir}~%"
                            #$output #$version)))))))))
    (native-inputs
     (list pkg-config))
    (home-page "https://github.com/smarco/WFA2-lib")
    (synopsis "Wavefront alignment algorithm library")
    (description "The wavefront alignment (WFA) algorithm is an exact
gap-affine algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process.")
    (properties `((tunable? . #t)))
    (license license:expat)))

(define-public vcflib
  (package
    (name "vcflib")
    (version "1.0.9")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/vcflib/vcflib")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0cmznzq7hl5vr504ww262rwz5lfdfrca5ksbcvwh3cgp44fiwykv"))
       (modules '((guix build utils)))
       (snippet
        #~(begin
            (substitute* "CMakeLists.txt"
              ((".*fastahack.*") "")
              ((".*smithwaterman.*") "")
              (("(pkg_check_modules\\(TABIXPP)" text)
               (string-append
                "pkg_check_modules(WFA2 REQUIRED libwfa2)\n"
                "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
                "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
                text))
              (("\\$\\{TABIXPP_LIBRARIES\\}" text)
               (string-append "${FASTAHACK_LIBRARIES} "
                              "${WFA2_LIBRARIES} "
                              "${SMITHWATERMAN_LIBRARIES} "
                              text)))
            (substitute* (find-files "." "\\.(h|c)(pp)?$")
              (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
              (("\"convert.h\"") "<smithwaterman/convert.h>")
              (("\"disorder.h\"") "<smithwaterman/disorder.h>")
              (("\"wavefront/wfa.hpp\"") "<wavefront/wfa.hpp>")
              (("Fasta.h") "fastahack/Fasta.h"))))))
    (build-system cmake-build-system)
    (inputs
     (list bzip2
           curl
           htslib
           fastahack
           perl
           python
           pybind11
           smithwaterman
           tabixpp
           xz
           zlib))
    (propagated-inputs
     (list wfa2-lib))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ;; Submodules.
       ;; This package builds against the .o files so we need to extract the source.
       ("filevercmp-src" ,(package-source filevercmp))
       ("fsom-src" ,(package-source fsom))
       ("intervaltree-src" ,(package-source intervaltree))
       ("multichoose-src" ,(package-source multichoose))))
    (arguments
     (list
      #:configure-flags
      #~(list "-DZIG=OFF"
              "-DTABIXPP_LOCAL=OFF"
              "-DTABIX_FOUND=ON"
              "-DWFA_GITMODULE=OFF"
              (string-append "-DPKG_CONFIG_EXECUTABLE="
                             (search-input-file
                              %build-inputs (string-append
                                             "/bin/" #$(pkg-config-for-target)))))
      #:tests? #f                       ; no tests
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'find-wfa2lib-headers
            (lambda _
              (setenv "CPLUS_INCLUDE_PATH"
                      (string-append
                       #$(this-package-input "wfa2-lib")
                       "/include/wfa2lib:"
                       (or (getenv "CPLUS_INCLUDE_PATH") "")))))
          (add-after 'unpack 'build-shared-library
            (lambda _
              (substitute* "CMakeLists.txt"
                (("vcflib STATIC") "vcflib SHARED"))))
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs native-inputs #:allow-other-keys)
              (let ((unpack (lambda (source target)
                              (mkdir-p target)
                              (with-directory-excursion target
                                (let ((source (or (assoc-ref inputs source)
                                                  (assoc-ref native-inputs source))))
                                  (if (file-is-directory? source)
                                      (copy-recursively source ".")
                                      (invoke "tar" "xvf"
                                              source
                                              "--strip-components=1")))))))
                (and
                 (unpack "filevercmp-src" "contrib/filevercmp")
                 (unpack "fsom-src" "contrib/fsom")
                 (unpack "intervaltree-src" "contrib/intervaltree")
                 (unpack "multichoose-src" "contrib/multichoose"))

                ;; This is needed for downstream packages to allow building
                ;; with GCC 11+.
                (substitute* "contrib/intervaltree/IntervalTree.h"
                  (("#include <vector>" m)
                   (string-append m "
#include <limits> /* std::numeric_limits */"))))))
          ;; This pkg-config file is provided by other distributions.
          (add-after 'install 'install-pkg-config-file
            (lambda _
              (let ((pkgconfig (string-append #$output "/lib/pkgconfig")))
                (mkdir-p pkgconfig)
                (with-output-to-file (string-append pkgconfig "/vcflib.pc")
                  (lambda _
                    (format #t "\
prefix=~a~@
exec_prefix=${prefix}~@
libdir=${exec_prefix}/lib~@
includedir=${prefix}/include~@
~@
Name: vcflib~@
Version: ~a~@
Requires: libwfa2, smithwaterman, fastahack, tabixpp~@
Description: C++ library for parsing and manipulating VCF files~@
Libs: -L${libdir} -lvcflib~@
Cflags: -I${includedir}~%"
                            #$output #$version)))))))))
    (home-page "https://github.com/vcflib/vcflib/")
    (synopsis "Library for parsing and manipulating VCF files")
    (description "Vcflib provides methods to manipulate and interpret
sequence variation as it can be described by VCF.  It is both an API for parsing
and operating on records of genomic variation as it can be described by the VCF
format, and a collection of command-line utilities for executing complex
manipulations on VCF files.")
    (license license:expat)))

(define-public freebayes
  (package
    (name "freebayes")
    (version "1.3.7")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/freebayes/freebayes")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32 "163nd1xkq547za80khlys4qkgal64f3sgl6ap3yvik68r0rgyisv"))))
    (build-system meson-build-system)
    (inputs
     (list fastahack htslib smithwaterman tabixpp vcflib))
    (native-inputs
     `(("bash-tap" ,bash-tap)
       ("bc" ,bc)
       ("grep" ,grep)   ; Built with perl support.
       ("parallel" ,parallel)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)
       ("python" ,python)
       ("samtools" ,samtools)
       ("simde" ,simde)
       ;; This submodule is needed to run the tests.
       ("test-simple-bash-src"
        ,(origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/ingydotnet/test-simple-bash/")
                 (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
           (file-name "test-simple-bash-src-checkout")
           (sha256
            (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-source
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((bash-tap (assoc-ref inputs "bash-tap")))
               (substitute* (find-files "test/t")
                 (("BASH_TAP_ROOT=bash-tap")
                  (string-append "BASH_TAP_ROOT=" bash-tap "/bin"))
                 (("bash-tap/bash-tap-bootstrap")
                  (string-append bash-tap "/bin/bash-tap-bootstrap"))
                 (("source.*bash-tap-bootstrap")
                  (string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
               (substitute* '("src/BedReader.cpp"
                              "src/BedReader.h")
                 (("../intervaltree/IntervalTree.h") "IntervalTree.h"))
               ;; We don't have Perl support in grep -E.
               (substitute* '("test/t/01_call_variants.t"
                              "test/t/01b_call_variants.t")
                 (("grep -P") "grep -E")
                 (("\\\\t") "	"))
               (substitute* "meson.build"
                 ;; Our pkg-config file is vcflib.pc
                 (("libvcflib") "vcflib")
                 (("vcflib_inc,") "")))))
         (add-after 'unpack 'unpack-submodule-sources
           (lambda* (#:key inputs #:allow-other-keys)
             (mkdir-p "test/test-simple-bash")
             (copy-recursively (assoc-ref inputs "test-simple-bash-src")
                               "test/test-simple-bash")))
        ;; The slow tests take longer than the specified timeout.
        ,@(if (any (cute string=? <> (%current-system))
                   '("armhf-linux" "aarch64-linux"))
            '((replace 'check
                (lambda* (#:key tests? #:allow-other-keys)
                  (when tests?
                    (invoke "meson" "test" "--timeout-multiplier" "5")))))
            '()))))
    (home-page "https://github.com/freebayes/freebayes")
    (synopsis "Haplotype-based variant detector")
    (description "FreeBayes is a Bayesian genetic variant detector designed to
find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
complex events (composite insertion and substitution events) smaller than the
length of a short-read sequencing alignment.")
    (license license:expat)))

(define-public samblaster
  (package
    (name "samblaster")
    (version "0.1.26")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/GregoryFaust/samblaster")
                    (commit (string-append "v." version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #f                       ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)           ;There is no configure phase.
          (replace 'install
            (lambda _
              (install-file "samblaster" (string-append #$output "/bin")))))))
    (home-page "https://github.com/GregoryFaust/samblaster")
    (synopsis "Mark duplicates in paired-end SAM files")
    (description "Samblaster is a fast and flexible program for marking
duplicates in read-id grouped paired-end SAM files.  It can also optionally
output discordant read pairs and/or split read mappings to separate SAM files,
and/or unmapped/clipped reads to a separate FASTQ file.  When marking
duplicates, samblaster will require approximately 20MB of memory per 1M read
pairs.")
    (license license:expat)))

(define-public r-velocyto
  (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
        (revision "1"))
    (package
      (name "r-velocyto")
      (version (git-version "0.6" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/velocyto-team/velocyto.R")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n"))))
      (build-system r-build-system)
      (inputs
       (list boost))
      (propagated-inputs
       (list r-hdf5r
             r-mass
             r-mgcv
             r-pcamethods
             r-rcpp
             r-rcpparmadillo
             ;; Suggested packages
             r-rtsne
             r-cluster
             r-abind
             r-h5
             r-biocgenerics
             r-genomicalignments
             r-rsamtools
             r-edger
             r-igraph))
      (home-page "https://velocyto.org")
      (synopsis "RNA velocity estimation in R")
      (description
       "This package provides basic routines for estimation of gene-specific
transcriptional derivatives and visualization of the resulting velocity
patterns.")
      (license license:gpl3))))

(define-public r-voltron
  (let ((commit "5057b703479239a9aaba761f07e65d849f6111f8")
        (revision "1"))
    (package
      (name "r-voltron")
      (version (git-version "1.0.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/BIMSBbioinfo/VoltRon")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1nximl4708a7fdwn8ysxpni3mp6dx33cphavlay7hh1pa55pnzgn"))
                (modules '((guix build utils)))
                ;; The tripack package is not available under a free license,
                ;; but interp provides free implementations of "tri.mesh" and
                ;; "neighbours".
                (snippet
                 '(substitute* '("DESCRIPTION" "NAMESPACE" "R/spatial.R")
                    (("tripack") "interp")))))
      (properties `((upstream-name . "VoltRon")))
      (build-system r-build-system)
      (inputs (list opencv tbb zlib))
      (propagated-inputs (list r-anndata
                               r-data-table
                               r-dplyr
                               r-ebimage
                               r-fastdummies
                               r-fnn
                               r-ggforce
                               r-ggplot2
                               r-ggpubr
                               r-ggrepel
                               r-hdf5r
                               r-htmltools
                               r-igraph
                               r-interp
                               r-irlba
                               r-magick
                               r-matrix
                               r-morpho
                               r-raster
                               r-rcpp
                               r-reshape2
                               r-rjson
                               r-rlang
                               r-s4vectors
                               r-scales
                               r-shiny
                               r-shinyjs
                               r-stringr
                               r-terra
                               r-umap
                               r-xml))
      (native-inputs (list pkg-config))
      (home-page "https://github.com/BIMSBbioinfo/VoltRon")
      (synopsis "VoltRon for Spatial Data Integration and Analysis")
      (description
       "@code{VoltRon} is a toolbox for spatial data analysis, multi-omics
integration using spatial image registration.  @code{VoltRon} is capable of
analyzing multiple types and modalities of spatially-aware datasets.
@code{VoltRon} visualizes and analyzes regions of interests (ROIs), spots,
cells and even molecules.")
      (license license:expat))))

(define-public methyldackel
  (package
    (name "methyldackel")
    (version "0.6.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dpryan79/MethylDackel")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "06kj76pyhzxfcjcpm840a3km3fa9994kfq4asglnb228pwak326z"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:test-target "test"
      #:make-flags
      #~(list "CC=gcc"
              "CFLAGS=-fcommon"
              "LIBBIGWIG=-lBigWig"
              (string-append "prefix=" #$output "/bin/"))
      #:phases
      '(modify-phases %standard-phases
         (replace 'configure
           (lambda _
             (substitute* "Makefile"
               (("install MethylDackel \\$\\(prefix\\)" match)
                (string-append "install -d $(prefix); " match))))))))
    (inputs
     (list curl htslib libbigwig zlib))
    ;; Needed for tests
    (native-inputs
     (list python-wrapper))
    (home-page "https://github.com/dpryan79/MethylDackel")
    (synopsis "Universal methylation extractor for BS-seq experiments")
    (description
     "MethylDackel will process a coordinate-sorted and indexed BAM or CRAM
file containing some form of BS-seq alignments and extract per-base
methylation metrics from them.  MethylDackel requires an indexed fasta file
containing the reference genome as well.")
    ;; See https://github.com/dpryan79/MethylDackel/issues/85
    (license license:expat)))

;; This package bundles PCRE 8.02 and cannot be built with the current
;; version.
(define-public phast
  (package
    (name "phast")
    (version "1.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/CshlSiepelLab/phast")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "10lpbllvny923jjbbyrpxahhd1m5h7sbj9gx7rd123rg10mlidki"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:make-flags
      #~(list "CC=gcc" (string-append "DESTDIR=" #$output))
      #:phases
      #~(modify-phases %standard-phases
          (replace 'configure
            (lambda* (#:key inputs outputs #:allow-other-keys)
              ;; Fix syntax
              (substitute* "test/Makefile"
                (("        ") "	"))
              (substitute* "Makefile"
                (("CLAPACKPATH=/usr/lib")
                 (string-append "CLAPACKPATH="
                                #$(this-package-input "clapack") "/lib")))
              ;; Renaming the libraries is not necessary with our version of
              ;; CLAPACK.
              (substitute* "src/lib/Makefile"
                (("ifdef CLAPACKPATH") "ifdef UNNECESSARY"))
              (substitute* "src/make-include.mk"
                (("-lblaswr") "-lblas")
                (("-ltmg") "-ltmglib")
                (("liblapack.a") "liblapack.so")
                (("libblas.a") "libblas.so")
                (("libf2c.a") "libf2c.so"))
              (substitute* "src/Makefile"
                (("/opt") "/share")
                (("/usr/") "/"))))
          (replace 'check
            (lambda _
              (setenv "PATH"
                      (string-append (getcwd) "/bin:" (getenv "PATH")))
              ;; Disable broken test
              (substitute* "test/Makefile"
                ((".*if.*hmrc_summary" m) (string-append "#" m)))
              ;; Only run the msa_view tests because the others fail for
              ;; unknown reasons.
              (invoke "make" "-C" "test" "msa_view"))))))
    (inputs
     (list clapack))
    (native-inputs
     (list perl))
    (home-page "http://compgen.cshl.edu/phast/")
    (synopsis "Phylogenetic analysis with space/time models")
    (description
     "Phylogenetic Analysis with Space/Time models (PHAST) is a collection of
command-line programs and supporting libraries for comparative and
evolutionary genomics.  Best known as the search engine behind the
Conservation tracks in the University of California, Santa Cruz (UCSC) Genome
Browser, PHAST also includes several tools for phylogenetic modeling,
functional element identification, as well as utilities for manipulating
alignments, trees and genomic annotations.")
    (license license:bsd-3)))

(define-public python-gffutils
  (package
    (name "python-gffutils")
    (version "0.10.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/daler/gffutils")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1gkzk7ps6w3ai2r81js9s9bzpba0jmxychnd2da6n9ggdnf2xzqz"))))
    (build-system python-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               ;; Tests need to access the HOME directory
               (setenv "HOME" "/tmp")
               (invoke "nosetests" "-a" "!slow")))))))
    (propagated-inputs
     (list python-argcomplete
           python-argh
           python-biopython
           python-pybedtools
           python-pyfaidx
           python-simplejson
           python-six))
    (native-inputs
     (list python-nose))
    (home-page "https://github.com/daler/gffutils")
    (synopsis "Tool for manipulation of GFF and GTF files")
    (description
     "python-gffutils is a Python package for working with and manipulating
the GFF and GTF format files typically used for genomic annotations.  The
files are loaded into a SQLite database, allowing much more complex
manipulation of hierarchical features (e.g., genes, transcripts, and exons)
than is possible with plain-text methods alone.")
    (license license:expat)))

(define-public indelfixer
  (package
    (name "indelfixer")
    (version "1.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/cbg-ethz/InDelFixer/")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "10ak05x8i1bx2p7rriv2rglqg1wr7c8wrhjrqlq1wm7ka99w8i79"))))
    (build-system ant-build-system)
    (arguments
     `(#:jar-name "InDelFixer.jar"
       #:source-dir "src/main/java"
       #:test-dir "src/test"))
    (inputs
     `(("java-commons-lang2" ,java-commons-lang)
       ("java-args4j" ,java-args4j)))
    (native-inputs
     (list java-junit))
    (home-page "https://github.com/cbg-ethz/InDelFixer/")
    (synopsis "Iterative and sensitive NGS sequence aligner")
    (description "InDelFixer is a sensitive aligner for 454, Illumina and
PacBio data, employing a full Smith-Waterman alignment against a reference.
This Java command line application aligns Next-Generation Sequencing (NGS) and
third-generation reads to a set of reference sequences, by a prior fast k-mer
matching and removes indels, causing frame shifts.  In addition, only a
specific region can be considered.  An iterative refinement of the alignment
can be performed, by alignment against the consensus sequence with wobbles.
The output is in SAM format.")
    (license license:gpl3+)))

(define-public libsbml
  (package
    (name "libsbml")
    (version "5.18.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/sbml/libsbml/"
                                  version "/stable/libSBML-"
                                  version "-core-src.tar.gz"))
              (sha256
               (base32
                "0slkagrk3nfi2qsksv6b1brj6zhx4bj4bkib2sdycvrcd10ql2lh"))))
    (build-system cmake-build-system)
    (arguments
     `(#:test-target "test"
       #:configure-flags
       ,#~(list "-DWITH_CHECK=ON"
                (string-append "-DLIBXML_LIBRARY="
                               #$(this-package-input "libxml2")
                               "/lib/libxml2.so")
                (string-append "-DLIBXML_INCLUDE_DIR="
                               #$(this-package-input "libxml2")
                               "/include/libxml2"))))
    (propagated-inputs
     (list libxml2))
    (native-inputs
     (list check swig))
    (home-page "https://sbml.org/Software/libSBML")
    (synopsis "Process SBML files and data streams")
    (description "LibSBML is a library to help you read, write, manipulate,
translate, and validate SBML files and data streams.  The @dfn{Systems Biology
Markup Language} (SBML) is an interchange format for computer models of
biological processes.  SBML is useful for models of metabolism, cell
signaling, and more.  It continues to be evolved and expanded by an
international community.")
    (license license:lgpl2.1+)))

(define-public kraken2
  (package
    (name "kraken2")
    (version "2.1.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/DerrickWood/kraken2")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1pl6ml1ldg2hnhy8ps56q0fl1wq3g91qkhinj6pb4yjjhv1rxsjf"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #false                  ; there are none
       #:make-flags
       ,#~(list "-C" "src"
                (string-append "KRAKEN2_DIR=" #$output "/bin"))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (add-before 'install 'install-scripts
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
                    (replacements `(("KRAKEN2_DIR" . ,bin)
                                    ("VERSION" . ,,version))))
               (mkdir-p bin)

               (with-directory-excursion "scripts"
                 (let ((scripts (find-files "." ".*")))
                   (substitute* scripts
                     (("#####=([^=]+)=#####" _ key)
                      (or (assoc-ref replacements key)
                          (error (format #false "unknown key: ~a~%" key)))))
                   (substitute* "kraken2"
                     (("compression_program = \"bzip2\"")
                      (string-append "compression_program = \""
                                     (which "bzip2")
                                     "\""))
                     (("compression_program = \"gzip\"")
                      (string-append "compression_program = \""
                                     (which "gzip")
                                     "\"")))
                   (substitute* '("download_genomic_library.sh"
                                  "download_taxonomy.sh"
                                  "16S_gg_installation.sh"
                                  "16S_silva_installation.sh"
                                  "16S_rdp_installation.sh")
                     (("wget") (which "wget")))
                   (substitute* '("download_taxonomy.sh"
			          "download_genomic_library.sh"
			          "rsync_from_ncbi.pl")
		     (("rsync -")
                      (string-append (which "rsync") " -")))
                   (substitute* "mask_low_complexity.sh"
                     (("which") (which "which")))
                   (substitute* '("mask_low_complexity.sh"
                                  "download_genomic_library.sh"
                                  "16S_silva_installation.sh")
                     (("sed -e ")
                      (string-append (which "sed") " -e ")))
                   (substitute* '("rsync_from_ncbi.pl"
                                  "16S_rdp_installation.sh"
                                  "16S_silva_installation.sh"
                                  "16S_gg_installation.sh"
                                  "download_taxonomy.sh"
                                  "download_genomic_library.sh")
                     (("gunzip") (which "gunzip")))
                   (for-each (lambda (script)
                               (chmod script #o555)
                               (install-file script bin))
                             scripts)))))))))
    (inputs
     (list gzip
           perl
           rsync
           sed
           wget
           which))
  (home-page "https://github.com/DerrickWood/kraken2")
  (synopsis "Taxonomic sequence classification system")
  (description "Kraken is a taxonomic sequence classifier that assigns
taxonomic labels to DNA sequences.  Kraken examines the k-mers within a query
sequence and uses the information within those k-mers to query a
database. That database maps k-mers to the lowest common ancestor (LCA) of all
genomes known to contain a given k-mer.")
  (license license:expat)))

(define-public lofreq
  (package
    (name "lofreq")
    (version "2.1.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/CSB5/lofreq")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0qssrn3mgjak7df6iqc1rljqd3g3a5syvg0lsv4vds43s3fq23bl"))))
    (build-system gnu-build-system)
    (arguments
     '(#:test-target "bug-tests"
       #:tests? #false ;test data are not included
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'set-source-file-times-to-1980
           (lambda _
             (let ((circa-1980 (* 10 366 24 60 60)))
               (for-each (lambda (file)
                           (let ((s (lstat file)))
                             (unless (eq? (stat:type s) 'symlink)
                               (utime file circa-1980 circa-1980))))
                         (find-files "." #:directories? #t))))))))
    (inputs
     (list htslib python-wrapper zlib))
    (native-inputs
     (list autoconf automake which))
    (home-page "https://csb5.github.io/lofreq/")
    (synopsis "Sensitive variant calling from sequencing data")
    (description "LoFreq is a fast and sensitive variant-caller for inferring
SNVs and indels from next-generation sequencing data.  It makes full use of
base-call qualities and other sources of errors inherent in
sequencing (e.g. mapping or base/indel alignment uncertainty), which are
usually ignored by other methods or only used for filtering.")
    (license license:expat)))

(define-public louvain
  (package
    (name "louvain")
    (version "0.2")
    (source (origin
              (method url-fetch)
              (uri "mirror://sourceforge/louvain/louvain_latest.tar.gz")
              (sha256
               (base32
                "0hqlv5jqc889nbv7j1bchrx4zhh69hgr2mqvfdygc7kwrywn22lb"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:tests? #false                   ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (add-after 'unpack 'patch-includes
            (lambda _
              (substitute* "main_community.cpp"
                (("using namespace std;" m)
                 (string-append "#include <unistd.h> /* for getpid */\n" m)))))
          (replace 'install
            (lambda _
              (for-each
               (lambda (exe)
                 (install-file exe (string-append #$output "/bin")))
               '("convert" "community" "hierarchy")))))))
    (home-page "https://sourceforge.net/projects/louvain/")
    (synopsis "Multi-criteria community detection")
    (description "This package offers a set of functions to use in order to
compute communities on graphs weighted or unweighted.")
    (license license:gpl3+)))

(define-public ivar
  (package
    (name "ivar")
    (version "1.4.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/andersen-lab/ivar")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0v3rsak84ilg4iaynwpmmkj507vham5rjk2pfsmylpaqylgc69yx"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:parallel-tests? #false          ;not supported
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'patch-CXXFLAGS
           (lambda _
             (substitute* '("src/Makefile.am"
                            "tests/Makefile.am")
               (("-Werror") "")))))))
    (inputs
     (list htslib zlib))
    (native-inputs
     (list autoconf automake))
    (home-page "https://andersen-lab.github.io/ivar/html/")
    (synopsis "Tools for amplicon-based sequencing")
    (description "iVar is a computational package that contains functions
broadly useful for viral amplicon-based sequencing.")
    (license license:gpl3+)))

(define-public python-pyliftover
  (package
    (name "python-pyliftover")
    (version "0.4")
    ;; The version of pypi does not include test data.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/konstantint/pyliftover")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1j8jp9iynv2l3jv5pr0pn0p3azlama1bqg233piglzm6bqh3m2m3"))))
    (build-system python-build-system)
    (arguments `(#:tests? #false)) ; the tests access the web
    (native-inputs
     (list python-pytest))
    (home-page "https://github.com/konstantint/pyliftover")
    (synopsis "Python implementation of UCSC liftOver genome coordinate conversion")
    (description
     "PyLiftover is a library for quick and easy conversion of genomic (point)
coordinates between different assemblies.")
    (license license:expat)))

(define-public python-cgatcore
  (package
    (name "python-cgatcore")
    (version "0.6.15")
    ;; The version of pypi does not include test data.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/cgat-developers/cgat-core")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "103hpdnkqr3a34blbicshk56j36g652s0g1zi9isppc5dngn0s18"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
      '(list "-k"
             (string-append
              ;; This test actually does what it should, but the check fails with
              ;; TypeError: cannot unpack non-iterable Namespace object
              "not test_start_and_stop_are_logged_with_argparse"
              ;; These all attempt to connect to localhost with SSH
              " and not test_job_should_use_TMPDIR_and_clean_up"
              " and not test_job_should_use_TMPDIR_and_clean_up_after_fail"
              " and not test_job_should_write_to_explicit_temp_and_not_clean_up"))
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'fix-references
           (lambda _
             (substitute* "cgatcore/pipeline/execution.py"
               (("#!/bin/bash") (string-append "#!" (which "bash")))
               (("executable=\"/bin/bash\"")
                (string-append "executable=\"" (which "bash") "\""))
               (("\\\\time") (which "time")))))
         (add-after 'unpack 'sqlite-compatibility
           (lambda _
             ;; Load apsw (and thus newer sqlite3) before importing Python's
             ;; older sqlite3 library.
             (substitute* "cgatcore/pipeline/__init__.py"
               (("import os")
                (string-append "import os\nimport apsw")))
             (substitute* "tests/template_pipeline.py"
               (("import sys" m)
                (string-append "import apsw\n" m))))))))
    (native-inputs
     (list python-pytest
           lsof
           inetutils
           openssl))
    (inputs (list time))
    (propagated-inputs
     (list python-apsw
           python-gevent
           python-pandas
           python-paramiko
           python-pyyaml
           python-ruffus
           python-sqlalchemy))
    (home-page "https://github.com/cgat-developers/cgat-core")
    (synopsis "Computational genomics analysis toolkit")
    (description
     "CGAT-core is a set of libraries and helper functions used to enable
researchers to design and build computational workflows for the analysis of
large-scale data-analysis.")
    (license license:expat)))

(define-public perl-cworld-dekker
  (package
    (name "perl-cworld-dekker")
    (version "1.01")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dekkerlab/cworld-dekker.git")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych"))))
    (build-system perl-build-system)
    (arguments
     (list
      #:modules '((guix build perl-build-system)
                  (guix build utils)
                  (srfi srfi-26))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'hardcode-references
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((bedtools #$(this-package-input "bedtools"))
                    (r #$(this-package-input "r-minimal")))
                (substitute* '("scripts/python/getEigenVectors.py"
                               "scripts/python/matrix2EigenVectors.py")
                  (("bedtools intersect")
                   (string-append bedtools "/bin/bedtools intersect")))
                (substitute* "lib/cworld/dekker.pm"
                  (("bedtools --version")
                   (string-append bedtools "/bin/bedtools --version")))
                (substitute* '("scripts/perl/correlateMatrices.pl"
                               "scripts/perl/matrix2scaling.pl"
                               "scripts/perl/matrix2distance.pl"
                               "scripts/perl/coverageCorrect.pl"
                               "scripts/perl/matrix2anchorPlot.pl"
                               "scripts/python/matrix2EigenVectors.py"
                               "scripts/python/matrix2insulation-lite.py"
                               "scripts/perl/matrix2compartment.pl"
                               "scripts/perl/anchorPurge.pl"
                               "scripts/perl/applyCorrection.pl"
                               "scripts/perl/compareInsulation.pl"
                               "scripts/perl/fillMissingData.pl"
                               "scripts/perl/matrix2loess.pl"
                               "scripts/python/getEigenVectors.py"
                               "scripts/perl/aggregateBED.pl"
                               "scripts/perl/collapseMatrix.pl"
                               "scripts/perl/matrix2direction.pl"
                               "scripts/perl/singletonRemoval.pl"
                               "lib/cworld/dekker.pm"
                               "scripts/perl/matrix2insulation.pl")
                  (("(`|\")Rscript" _ pre)
                   (string-append pre r "/bin/Rscript"))))))
          (add-after 'install 'install-scripts
            (lambda _
              (let ((share (string-append #$output "/share/cworld-dekker")))
                (mkdir-p share)
                (copy-recursively "scripts" share)

                ;; Make all scripts executable and wrap them.
                (let ((r     (find-files share "\\.R$"))
                      (py    (find-files share "\\.py$"))
                      (pl    (find-files share "\\.pl$"))
                      (wrap  (lambda* (script var #:optional (extra ""))
                               (let ((path (string-append (getenv var)
                                                          extra)))
                                 (wrap-program script
                                   `(,var ":" prefix (,path)))))))
                  (for-each (cut chmod <> #o555) (append r py pl))
                  (for-each (cut wrap <> "PERL5LIB"
                                 (string-append ":" #$output
                                                "/lib/perl5/site_perl"))
                            pl)
                  (for-each (cut wrap <> "GUIX_PYTHONPATH") py))))))))
    (inputs
     (list gd
           perl-gd
           bedtools
           python-wrapper
           python-scipy
           python-numpy
           python-matplotlib
           python-h5py
           python-scikit-learn
           r-minimal))
    (native-inputs
     (list perl-module-build))
    (home-page "https://github.com/dekkerlab/cworld-dekker")
    (synopsis "Utility and analysis scripts for 3C, 4C, 5C, and Hi-C data")
    (description "This package is a collection of Perl, Python, and R
scripts for manipulating 3C/4C/5C/Hi-C data.")
    (license license:asl2.0)))

(define-public ensembl-vep
  (let* ((api-version "112")
         (api-module
          (lambda (name hash)
            (origin (method git-fetch)
                    (uri (git-reference
                          (url (string-append "https://github.com/Ensembl/"
                                              name ".git"))
                          (commit (string-append "release/" api-version))))
                    (file-name (string-append name "-" api-version "-checkout"))
                    (sha256 (base32 hash))))))
    (package
      (name "ensembl-vep")
      (version api-version)
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/Ensembl/ensembl-vep.git")
               (commit (string-append "release/" version))))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0nznmiln2q6bzd3xp8d5cw56higa5w3g9rmg66956bkfky53chvw"))))
      (build-system gnu-build-system)
      (arguments
       `(#:modules ((guix build gnu-build-system)
                    (guix build utils)
                    (ice-9 match))
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (delete 'build)
           ;; Tests need to run after installation
           (delete 'check)
           (replace 'install
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let* ((modules '(("ensembl" "/")
                                 ("ensembl-variation" "/Variation")
                                 ("ensembl-funcgen"   "/Funcgen")
                                 ("ensembl-io"        "/")))
                      (scripts '(("convert_cache.pl" "vep_convert_cache.pl")
                                 ("INSTALL.pl"       "vep_install.pl")
                                 ("haplo"            #f)
                                 ("variant_recoder"  #f)
                                 ("filter_vep"       #f)
                                 ("vep"              #f)))
                      (out  (assoc-ref outputs "out"))
                      (bin  (string-append out "/bin"))
                      (perl (string-append out "/lib/perl5/site_perl")))
                 (for-each
                  (match-lambda
                    ((name path)
                     (let ((dir (string-append perl "/Bio/EnsEMBL" path)))
                       (mkdir-p dir)
                       (copy-recursively
                        (string-append (assoc-ref inputs (string-append "api-module-" name))
                                       "/modules/Bio/EnsEMBL" path)
                        dir))))
                  modules)
                 (copy-recursively "modules/" perl)
                 (mkdir-p bin)
                 (for-each
                  (match-lambda
                    ((script new-name)
                     (let ((location (string-append bin "/"
                                                    (or new-name (basename script)))))
                       (copy-file script location)
                       (chmod location #o555)
                       (wrap-program location
                         `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")
                                                  ,perl))))))
                  scripts)

                 ;; Fix path to tools
                 (with-directory-excursion (string-append perl "/Bio/EnsEMBL")
                   (substitute* '("Funcgen/RunnableDB/ProbeMapping/PrePipelineChecks.pm"
                                  "VEP/BaseRunner.pm"
                                  "VEP/Utils.pm"
                                  "VEP/AnnotationSource/Cache/VariationTabix.pm"
                                  "VEP/AnnotationSource/Cache/BaseSerialized.pm"
                                  "Variation/Utils/BaseVepTabixPlugin.pm"
                                  "Variation/Utils/VEP.pm"
                                  "Variation/Pipeline/ReleaseDataDumps/PreRunChecks.pm")
                     (("`which")
                      (string-append "`"
                                     (assoc-ref inputs "which")
                                     "/bin/which")))))))
           (add-after 'install 'check
             (lambda* (#:key tests? inputs outputs #:allow-other-keys)
               (when tests?
                 (setenv "PERL5LIB"
                         (string-append (getenv "PERL5LIB")
                                        ":"
                                        (assoc-ref outputs "out")
                                        "/lib/perl5/site_perl"))
                 (copy-recursively (string-append (assoc-ref inputs "source") "/t")
                                   "/tmp/t")
                 (for-each make-file-writable (find-files "/tmp/t"))
                 ;; TODO: haplo needs Set/IntervalTree.pm
                 (invoke "perl" "-e" (string-append "
use Test::Harness; use Test::Exception;
my $dirname = \"/tmp\";
opendir TEST, \"$dirname\\/t\";
my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir TEST; closedir TEST;
@test_files = grep {!/Haplo/} @test_files;
runtests(@test_files);
"))))))))
      (inputs
       (list bioperl-minimal
             perl-bio-db-hts
             perl-dbi
             perl-dbd-mysql
             perl-libwww
             perl-list-moreutils
             perl-http-tiny
             perl-json
             which))
      (propagated-inputs
       (list kentutils))
      (native-inputs
       `(("unzip" ,unzip)
         ("perl" ,perl)
         ("api-module-ensembl"
          ,(api-module "ensembl"
                       "10r576iqrz1p61mqbbfs87w4w3nldi45p51z52mq76f3n00l010h"))
         ("api-module-ensembl-variation"
          ,(api-module "ensembl-variation"
                       "0ad03xnyyqpya1bkg6igq9abqxdmi58j89wn2kb3m4bvy1zs03mf"))
         ("api-module-ensembl-funcgen"
          ,(api-module "ensembl-funcgen"
                       "1m3dxnr6k9x5hmcsxckpxlqx7vbc82lk74r84vcjijgxjkfa5rpp"))
         ("api-module-ensembl-io"
          ,(api-module "ensembl-io"
                       "1xr6kdqqzmbi3m4bls589d1dfjvbs13dxlbf1y172xjyipvmag43"))
         ("perl-test-deep" ,perl-test-deep)
         ("perl-test-exception" ,perl-test-exception)
         ("perl-test-harness" ,perl-test-harness)
         ("perl-test-warnings" ,perl-test-warnings)))
      (home-page "http://www.ensembl.org/vep")
      (synopsis "Predict functional effects of genomic variants")
      (description
       "This package provides a Variant Effect Predictor, which predicts
the functional effects of genomic variants.  It also provides
Haplosaurus, which uses phased genotype data to predict
whole-transcript haplotype sequences, and Variant Recoder, which
translates between different variant encodings.")
      (license license:asl2.0))))

(define-public r-signac
  (let ((commit "8ecdde291676102bb3b503f48926c993354b5471")
        (revision "1"))
    (package
      (name "r-signac")
      (version (git-version "1.12.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/timoast/signac/")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0idkcqb1i13m164nxbdwgs3vflw0cxzm2ir84aw0i811vx9lqz8c"))))
      (properties `((upstream-name . "Signac")))
      (build-system r-build-system)
      (inputs (list zlib))
      (propagated-inputs
       (list r-biocgenerics
             r-data-table
             r-dplyr
             r-fastmatch
             r-future
             r-future-apply
             r-genomeinfodb
             r-genomicranges
             r-ggplot2
             r-iranges
             r-irlba
             r-matrix
             r-patchwork
             r-pbapply
             r-rcpp
             r-rcpproll
             r-rsamtools
             r-s4vectors
             r-scales
             r-seuratobject
             r-stringi
             r-tidyr
             r-tidyselect
             r-vctrs))
      (home-page "https://github.com/timoast/signac/")
      (synopsis "Analysis of single-cell chromatin data")
      (description
       "This package provides a framework for the analysis and exploration of
single-cell chromatin data.  The Signac package contains functions for
quantifying single-cell chromatin data, computing per-cell quality control
metrics, dimension reduction and normalization, visualization, and DNA
sequence motif analysis.")
      (license license:expat))))

(define-public tombo
  (package
    (name "tombo")
    (version "1.5.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "ont-tombo" version))
       (sha256
        (base32
         "1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm"))))
    (build-system python-build-system)
    (arguments
     '(#:tests? #false))                ;no tests
    (native-inputs
     (list python-cython python-nose2))
    ;; The package mainly consists of a command-line tool, but also has a
    ;; Python-API. Thus these must be propagated.
    (propagated-inputs
     (list python-future
           python-h5py
           python-mappy
           python-numpy
           python-scipy
           python-tqdm
           python-rpy2))
    (home-page "https://github.com/nanoporetech/tombo")
    (synopsis "Analysis of raw nanopore sequencing data")
    (description "Tombo is a suite of tools primarily for the identification of
modified nucleotides from nanopore sequencing data.  Tombo also provides tools
for the analysis and visualization of raw nanopore signal.")
    ;; Some parts may be BSD-3-licensed.
    (license license:mpl2.0)))

(define-public python-pyvcf
  (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
        (revision "0"))
    (package
      (name "python-pyvcf")
      (version (git-version "0.6.8" revision commit))
      ;; Use git, because the PyPI tarballs lack test data.
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/jamescasbon/PyVCF.git")
               ;; Latest release is not tagged.
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
      (build-system python-build-system)
      (arguments
       `(#:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'patch-sample-script
             (lambda _
               ;; Add Python 3 compatibility to this sample script.
               (substitute* "scripts/vcf_sample_filter.py"
                 (("print (.*)\n" _ arg)
                  (string-append "print(" arg ")\n")))))
           (add-after 'install 'remove-installed-tests
             ;; Do not install test files.
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (delete-file-recursively (string-append
                                         (site-packages inputs outputs)
                                         "/vcf/test")))))))
      (native-inputs
       ;; Older setuptools is needed for use_2to3.
       (list python-cython python-setuptools-57))
      (propagated-inputs
       (list python-pysam python-rpy2))
      (home-page "https://github.com/jamescasbon/PyVCF")
      (synopsis "Variant Call Format parser for Python")
      (description "This package provides a @acronym{VCF,Variant Call Format}
parser for Python.")
      (license license:expat))))

(define-public nanosv
  (package
   (name "nanosv")
   (version "1.2.4")
   (source (origin
            (method url-fetch)
            (uri (pypi-uri "NanoSV" version))
            (sha256
             (base32
              "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
   (build-system python-build-system)
   (inputs
    (list python-configparser python-pysam python-pyvcf))
   (home-page "https://github.com/mroosmalen/nanosv")
   (synopsis "Structural variation detection tool for Oxford Nanopore data")
   (description "NanoSV is a software package that can be used to identify
structural genomic variations in long-read sequencing data, such as data
produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION
instruments, or Pacific Biosciences RSII or Sequel sequencers.")
   (license license:expat)))

(define-public python-strawc
  (package
    (name "python-strawc")
    (version "0.0.2.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "strawC" version))
       (sha256
        (base32
         "1z1gy8n56lhriy6hdkh9r82ndikndipq2cy2wh8q185qig4rimr6"))))
    (build-system python-build-system)
    (inputs
     (list curl zlib))
    (propagated-inputs
     (list pybind11))
    (home-page "https://github.com/aidenlab/straw")
    (synopsis "Stream data from .hic files")
    (description "Straw is library which allows rapid streaming of contact
data from @file{.hic} files.  This package provides Python bindings.")
    (license license:expat)))

(define-public python-pybbi
  (package
    (name "python-pybbi")
    (version "0.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pybbi" version))
       (sha256
        (base32
         "1hvy2f28i2b41l1pq15vciqbj538n0lichp8yr6413jmgg06xdsk"))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #false ; tests require network access
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'set-cc
           (lambda _ (setenv "CC" "gcc")))
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (copy-recursively "tests" "/tmp/tests")
               (with-directory-excursion "/tmp/tests"
                 (invoke "python" "-m" "pytest" "-v"))))))))
    (native-inputs
     (list pkg-config python-pkgconfig python-pytest))
    (inputs
     (list libpng openssl zlib))
    (propagated-inputs
     (list python-cython python-numpy python-pandas python-six))
    (home-page "https://github.com/nvictus/pybbi")
    (synopsis "Python bindings to UCSC Big Binary file library")
    (description
     "This package provides Python bindings to the UCSC Big
Binary (bigWig/bigBed) file library.  This provides read-level access to local
and remote bigWig and bigBed files but no write capabilitites.  The main
feature is fast retrieval of range queries into numpy arrays.")
    (license license:expat)))

(define-public python-dna-features-viewer
  (package
    (name "python-dna-features-viewer")
    (version "3.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "dna_features_viewer" version))
       (sha256
        (base32
         "10a5pmh73spdgfml88zjqg1rn2j2zdxn06ir8a5q3arspyqvyqcb"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:tests? #false ;there are none
      #:phases
      '(modify-phases %standard-phases
         ;; See https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/73
         ;; and https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/74
         (add-after 'unpack 'fix-biopython-compatibility
           (lambda _
             (substitute* "dna_features_viewer/biotools.py"
               (("zip\\(aa1 \\+ \"\\*\", aa3 \\+ \\[\"\\*\"\\]\\)")
                "zip(aa1 + ('*',), aa3 + ('*',))")))))))
    (propagated-inputs
     (list python-biopython
           python-matplotlib
           python-packaging))
    (home-page
     "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer")
    (synopsis "Plot features from DNA sequences")
    (description
     "DNA Features Viewer is a Python library to visualize DNA features,
e.g. from GenBank or Gff files, or Biopython SeqRecords.")
    (license license:expat)))

(define-public python-coolbox
  (package
    (name "python-coolbox")
    (version "0.3.8")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "coolbox" version))
       (sha256
        (base32
         "0gqp76285w9klswr47y6kxbzwhv033b26jfa179kccfhiaq5p2xa"))))
    (build-system python-build-system)
    (arguments '(#:tests? #false)) ; there are none
    (inputs
     (list pybind11))
    (propagated-inputs
     (list python-cooler
           python-dna-features-viewer
           python-fire
           python-h5py
           python-intervaltree
           python-ipywidgets
           jupyter
           python-matplotlib
           python-nbformat
           python-numpy
           python-numpydoc
           python-pandas
           python-pybbi
           python-pytest
           python-scipy
           python-statsmodels
           python-strawc
           python-svgutils
           python-termcolor
           python-voila))
    (home-page "https://github.com/GangCaoLab/CoolBox")
    (synopsis "Genomic data visualization toolkit")
    (description
     "CoolBox is a toolkit for visual analysis of genomics data.  It aims to
be highly compatible with the Python ecosystem, easy to use and highly
customizable with a well-designed user interface.  It can be used in various
visualization situations, for example, to produce high-quality genome track
plots or fetch common used genomic data files with a Python script or command
line, interactively explore genomic data within Jupyter environment or web
browser.")
    (license license:gpl3+)))

(define-public python-pyspoa
  (package
    (name "python-pyspoa")
    (version "0.0.5")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/nanoporetech/pyspoa")
             (commit (string-append "v" version))
             (recursive? #true)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1lgf2shzhxkcsircd6vy46h27pjljd5q95fyz1cm3lkk702qbnzx"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'build-libspoa
           (lambda _
             (mkdir-p "src/build")
             (with-directory-excursion "src/build"
               (invoke "cmake"
                       "-Dspoa_optimize_for_portability=ON"
                       "-DCMAKE_BUILD_TYPE=Release"
                       "-DCMAKE_CXX_FLAGS=\"-I ../vendor/cereal/include/\" -fPIC"
                       "..")
               (invoke "make"))))
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (invoke "python" "tests/test_pyspoa.py")))))))
    (propagated-inputs
     (list pybind11))
    (native-inputs
     `(("cmake" ,cmake-minimal)))
    (home-page "https://github.com/nanoporetech/pyspoa")
    (synopsis "Python bindings for the SIMD partial order alignment library")
    (description
     "This package provides Python bindings for spoa, a C++ implementation of
the @dfn{partial order alignment} (POA) algorithm (as described in
10.1093/bioinformatics/18.3.452) which is used to generate consensus
sequences")
    (license license:expat)))

(define-public python-bwapy
  (package
    (name "python-bwapy")
    (version "0.1.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "bwapy" version))
       (sha256
        (base32 "090qwx3vl729zn3a7sksbviyg04kc71gpbm3nd8dalqp673x1npw"))
       (modules '((guix build utils)))
       (snippet
        '(for-each delete-file (find-files "." "\\.o$")))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "setup.py"
               (("wheel>=0.34") "wheel>=0.30"))))
         ;; TODO: it's possible that the import error points to a real
         ;; problem with the C sources.
         (delete 'sanity-check))))
    (propagated-inputs
     (list python-cffi python-setuptools python-wheel))
    (inputs
     (list zlib))
    (home-page "https://github.com/ACEnglish/bwapy")
    (synopsis "Python bindings to bwa aligner")
    (description "This package provides Python bindings to the bwa mem
aligner.")
    ;; These Python bindings are licensed under Mozilla Public License 2.0,
    ;; bwa itself is licenced under GNU General Public License v3.0.
    (license license:mpl2.0)))

(define-public scvelo
  (package
    (name "scvelo")
    (version "0.2.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scvelo" version))
       (sha256
        (base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z"))))
    (build-system pyproject-build-system)
    (arguments
     (list
       #:test-flags
       ;; XXX: these two tests fail for unknown reasons
       '(list "-k" "not test_perfect_fit and not test_perfect_fit_2d")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'matplotlib-compatibility
             (lambda _
               (substitute* "scvelo/settings.py"
                 (("warnings.filterwarnings\\(\"ignore\", category=cbook.mplDeprecation\\)")
                  ""))))
           ;; Numba needs a writable dir to cache functions.
           (add-before 'check 'set-numba-cache-dir
             (lambda _
               (setenv "NUMBA_CACHE_DIR" "/tmp")))
           (replace 'check
             (lambda* (#:key tests? test-flags #:allow-other-keys)
               (when tests?
                 ;; The discovered test file names must match the names of the
                 ;; compiled files, so we cannot run the tests from
                 ;; /tmp/guix-build-*.
                 (with-directory-excursion
                     (string-append #$output
                                    "/lib/python3.10/site-packages/scvelo/core/tests/")
                   (apply invoke "pytest" "-v" test-flags))))))))
    (propagated-inputs
     (list python-anndata
           python-hnswlib
           python-isort
           python-igraph
           python-loompy
           python-louvain
           python-matplotlib
           python-numba
           python-numpy
           python-pandas
           python-scanpy
           python-scikit-learn
           python-scipy
           python-umap-learn
           pybind11))
    (native-inputs
     (list python-black
           python-flake8
           python-hypothesis
           python-pytest
           python-setuptools-scm
           python-wheel))
    (home-page "https://scvelo.org")
    (synopsis "RNA velocity generalized through dynamical modeling")
    (description "ScVelo is a scalable toolkit for RNA velocity analysis in
single cells.  RNA velocity enables the recovery of directed dynamic
information by leveraging splicing kinetics. scVelo generalizes the concept of
RNA velocity by relaxing previously made assumptions with a stochastic and a
dynamical model that solves the full transcriptional dynamics.  It thereby
adapts RNA velocity to widely varying specifications such as non-stationary
populations.")
    (license license:bsd-3)))

(define-public scregseg
  (package
    (name "scregseg")
    (version "0.1.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/BIMSBbioinfo/scregseg")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "07g2barywa1wi8mggbxkbxqjw1fzd0a0l9cjdbkx4s40imb1dbxb"))
              (snippet
               '(delete-file "src/scregseg/_utils.c"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      '(modify-phases %standard-phases
         ;; Numba needs a writable dir to cache functions.
         (add-before 'check 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp")))
         ;; Cython extensions have to be built before running the tests.
         (add-before 'check 'build-extensions
           (lambda _
             (invoke "python" "setup.py" "build_ext" "--inplace")))
         (add-after 'unpack 'do-not-fail-to-find-sklearn
           (lambda _
             ;; XXX: I have no idea why it cannot seem to find sklearn.
             (substitute* "setup.py"
               (("'sklearn',") "")))))))
    (native-inputs
     (list python-cython))
    (propagated-inputs
     (list python-scikit-learn
           python-scipy
           python-numpy
           python-hmmlearn
           python-pandas
           python-numba
           python-anndata
           python-scanpy
           python-pybedtools
           python-pysam
           python-matplotlib
           python-seaborn
           python-coolbox))
    (home-page "https://github.com/BIMSBbioinfo/scregseg")
    (synopsis "Single-cell regulatory landscape segmentation")
    (description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a
tool that facilitates the analysis of single cell ATAC-seq data by an
HMM-based segmentation algorithm.  Scregseg uses an HMM with
Dirichlet-Multinomial emission probabilities to segment the genome either
according to distinct relative cross-cell accessibility profiles or (after
collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct
cross-cluster accessibility profiles.")
    (license license:gpl3+)))

(define-public megadepth
  (package
    (name "megadepth")
    (version "1.1.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/ChristopherWilks/megadepth")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0hj69d2dgmk2zwgazik7xzc04fxxlk93p888kpgc52fmhd95qph7"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #false ; some tests seem to require connection to
                       ; www.ebi.ac.uk; this may be caused by htslib.
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'prepare-CMakeLists.txt
           (lambda _
             (rename-file "CMakeLists.txt.ci" "CMakeLists.txt")
             (substitute* "CMakeLists.txt"
               (("`cat ../VERSION`") ,version)
               (("target_link_libraries\\(megadepth_static") "#")
               (("target_link_libraries\\(megadepth_statlib") "#")
               (("add_executable\\(megadepth_static") "#")
               (("add_executable\\(megadepth_statlib") "#"))

             (substitute* "tests/test.sh"
               ;; Disable remote test
               (("./megadepth http://stingray.cs.jhu.edu/data/temp/test.bam") "#")
               ;; Prior to installation the binary's name differs from what
               ;; the test script assumes.
               (("./megadepth") "../build/megadepth_dynamic"))))
         (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
             (when tests?
               (with-directory-excursion "../source"
                 (invoke "bash" "tests/test.sh" "use-local-test-data")))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (mkdir-p bin)
               (copy-file "megadepth_dynamic"
                          (string-append bin "/megadepth"))))))))
    (native-inputs
     (list diffutils perl grep))
    (inputs
     (list curl htslib libdeflate libbigwig zlib))
    (home-page "https://github.com/ChristopherWilks/megadepth")
    (synopsis "BigWig and BAM/CRAM related utilities")
    (description "Megadepth is an efficient tool for extracting coverage
related information from RNA and DNA-seq BAM and BigWig files.  It supports
reading whole-genome coverage from BAM files and writing either indexed TSV or
BigWig files, as well as efficient region coverage summary over intervals from
both types of files.")
    (license license:expat)))

(define-public megahit
  (package
    (name "megahit")
    (version "1.2.9")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/voutcn/megahit.git")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:test-target "simple_test"
      #:phases
      '(modify-phases %standard-phases
         (add-after 'unpack 'fix-tests
           (lambda _
             (substitute* "src/megahit"
               (("os.path.join\\(script_path, '..'\\)")
                "os.path.join(script_path, '../source')")))))))
    (inputs (list python-wrapper zlib))
    (home-page "https://www.ncbi.nlm.nih.gov/pubmed/25609793")
    (synopsis "Meta-genome assembler")
    (description "Megahit is a fast and memory-efficient NGS assembler.  It is
optimized for metagenomes, but also works well on generic single genome
assembly (small or mammalian size) and single-cell assembly.")
    (license license:gpl3)))

(define-public mudskipper
  (package
    (name "mudskipper")
    (version "0.1.0")
    (source (origin
              (method url-fetch)
              (uri (crate-uri "mudskipper" version))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "1y7fnlz6irmxdmv6bxzm95w4ws4vzldlrh8npvgxmdnrz9pgb1dv"))))
    (build-system cargo-build-system)
    (arguments
     `(#:tests? #false    ;fail because the "mudskipper" crate cannot be found
       #:cargo-inputs
       (("rust-bio" ,rust-bio-0.39)
        ("rust-bio-types" ,rust-bio-types-0.12)
        ("rust-clap" ,rust-clap-2)
        ("rust-coitrees" ,rust-coitrees-0.2)
        ("rust-env-logger" ,rust-env-logger-0.9)
        ("rust-fnv" ,rust-fnv-1)
        ("rust-indicatif" ,rust-indicatif-0.16)
        ("rust-libradicl" ,rust-libradicl-0.4)
        ("rust-linecount" ,rust-linecount-0.1)
        ("rust-log" ,rust-log-0.4)
        ("rust-num-cpus" ,rust-num-cpus-1)
        ("rust-rust-htslib" ,rust-rust-htslib-0.38))))
    (native-inputs
     (list cmake-minimal pkg-config))
    (inputs
     (list zlib xz))
    (home-page "https://github.com/OceanGenomics/mudskipper")
    (synopsis "Convert genomic alignments to transcriptomic BAM/RAD files")
    (description "Mudskipper is a tool for projecting genomic alignments to
transcriptomic coordinates.")
    (license license:bsd-3)))

(define-public r-ascat
  (package
   (name "r-ascat")
   (version "2.5.2")
   (source (origin
            (method git-fetch)
            (uri (git-reference
                  (url "https://github.com/Crick-CancerGenomics/ascat.git")
                  (commit (string-append "v" version))))
            (file-name (git-file-name name version))
            (sha256
             (base32
              "0cc0y3as6cb64iwnx0pgbajiig7m4z723mns9d5i4j09ccid3ccm"))))
   (build-system r-build-system)
   (arguments
    `(#:phases
      (modify-phases %standard-phases
       (add-after 'unpack 'move-to-ascat-dir
         (lambda _
           (chdir "ASCAT"))))))
   (propagated-inputs
    (list r-rcolorbrewer))
   (home-page "https://github.com/VanLoo-lab/ascat/")
   (synopsis "Allele-Specific Copy Number Analysis of Tumors in R")
   (description "This package provides the @acronym{ASCAT,Allele-Specific Copy
Number Analysis of Tumors} R package that can be used to infer tumour purity,
ploidy and allele-specific copy number profiles.")
   (license license:gpl3)))

(define-public r-battenberg
  (package
   (name "r-battenberg")
   (version "2.2.9")
   (source (origin
            (method git-fetch)
            (uri (git-reference
                  (url "https://github.com/Wedge-lab/battenberg.git")
                  (commit (string-append "v" version))))
            (file-name (git-file-name name version))
            (sha256
             (base32
              "0nmcq4c7y5g8h8lxsq9vadz9bj4qgqn118alip520ny6czaxki4h"))))
   (build-system r-build-system)
   (propagated-inputs
    (list r-devtools
          r-readr
          r-doparallel
          r-ggplot2
          r-rcolorbrewer
          r-gridextra
          r-gtools
          r-ascat))
   (home-page "https://github.com/Wedge-lab/battenberg")
   (synopsis "Subclonal copy number estimation in R")
   (description "This package contains the Battenberg R package for subclonal
copy number estimation, as described by
@url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}")
   (license license:gpl3)))

(define-public r-catch
  (let ((commit "196ddd5a51b1a5f5daa01de53fdaad9b7505e084")
        (revision "1"))
    (package
      (name "r-catch")
      (version (git-version "1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/zhanyinx/CaTCH")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "11c7f1fc8f57wnwk1hrgr5y814m80zj8gkz5021vxyxy2v02cqgd"))))
      (build-system r-build-system)
      (arguments
       `(#:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'chdir
             (lambda _ (chdir "CaTCH"))))))
      (home-page "https://github.com/zhanyinx/CaTCH_R")
      (synopsis "Call a hierarchy of domains based on Hi-C data")
      (description "This package allows building the hierarchy of domains
starting from Hi-C data.  Each hierarchical level is identified by a minimum
value of physical insulation between neighboring domains.")
      (license license:gpl2+))))

(define-public r-spacexr
  (let ((commit "0a0861e3d1e16014a20e9b743d0e19d3b42231f3")
        (revision "1"))
    (package
      (name "r-spacexr")
      (version (git-version "2.2.1" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/dmcable/spacexr")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0hqrllzq2hi6dsr8nykn1yp7s3rcbjrv3m624b61n4nxnzza458a"))))
      (properties `((upstream-name . "spacexr")))
      (build-system r-build-system)
      (propagated-inputs (list r-compquadform
                               r-data-table
                               r-doparallel
                               r-dplyr
                               r-fields
                               r-foreach
                               r-ggplot2
                               r-knitr
                               r-locfdr
                               r-matrix
                               r-metafor
                               r-mgcv
                               r-pals
                               r-quadprog
                               r-readr
                               r-reshape2
                               r-rfast
                               r-rmarkdown
                               r-tibble))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/dmcable/spacexr")
      (synopsis
       "Cell type identification and differential expression in spatial transcriptomics")
      (description
       "This package is used for cell type identification in spatial transcriptomics.
It also handles cell type-specific differential expression.")
      (license license:gpl3))))

(define-public r-spectre
  (let ((commit "f6648ab3eb9499300d86502b5d60ec370ae9b61a")
        (revision "1"))
    (package
      (name "r-spectre")
      (version (git-version "0.5.5" revision commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/ImmuneDynamics/Spectre")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0g38grrhbqqa4bmcilvdyawbkcnax6k4vffx2giywp18mbirmj0x"))))
      (properties `((upstream-name . "Spectre")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-biobase
             r-biocmanager
             r-caret
             r-class
             r-colorramps
             r-data-table
             r-devtools
             r-dplyr
             r-exactextractr
             r-factoextra
             r-flowcore
             r-flowsom
             r-flowviz
             r-fnn
             r-ggplot2
             r-ggpointdensity
             r-ggpubr
             r-ggraph
             r-ggthemes
             r-gridextra
             r-gridextra
             r-gtools
             r-hdf5array
             r-irlba
             r-pheatmap
             r-plyr
             r-qs
             r-raster
             r-rcolorbrewer
             r-rgeos
             r-rhdf5
             r-rstudioapi
             r-rsvd
             r-rtsne
             r-s2
             r-scales
             r-sf
             r-sp
             r-stars
             r-stringr
             r-tidygraph
             r-tidyr
             r-tidyr
             r-tiff
             r-umap))
      (home-page "https://github.com/ImmuneDynamics/Spectre")
      (synopsis "High-dimensional cytometry and imaging analysis")
      (description
       "This package provides a computational toolkit in R for the
integration, exploration, and analysis of high-dimensional single-cell
cytometry and imaging data.")
      (license license:expat))))

(define-public r-compgenomrdata
  (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")
        (revision "1"))
    (package
      (name "r-compgenomrdata")
      (version (git-version "0.1.0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/compgenomr/compGenomRData")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "06gdvz4m4qlb1ylv10qfx09zv4c95cm7nps4y2s67m946kv8czv8"))))
      (properties `((upstream-name . "compGenomRData")))
      (build-system r-build-system)
      (home-page "https://github.com/compgenomr/compGenomRData")
      (synopsis "Data for Computational Genomics with R book")
      (description "This package provides data for the book \"Computational
Genomics with R\".")
      (license license:gpl3))))

(define-public r-cytonorm
  (let ((commit "166f9ff3d692278241018c2846cb4f86ab16065b")
        (revision "1"))
    (package
      (name "r-cytonorm")
      (version (git-version "0.0.10" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/saeyslab/CytoNorm")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0vbqy3b26j1zqmwgqx59kkn9pm2m0qwlcppskvahrxcwrj6m1s5y"))))
      (properties `((upstream-name . "CytoNorm")))
      (build-system r-build-system)
      (propagated-inputs
       (list r-cytoml
             r-dplyr
             r-emdist
             r-flowcore
             r-flowsom
             r-flowworkspace
             r-ggplot2
             r-gridextra
             r-pheatmap
             r-stringr))
      (home-page "https://github.com/saeyslab/CytoNorm")
      (synopsis "Normalize cytometry data measured across multiple batches")
      (description
       "This package can be used to normalize cytometry samples when a control
sample is taken along in each of the batches.  This is done by first
identifying multiple clusters/cell types, learning the batch effects from the
control samples and applying quantile normalization on all markers of
interest.")
      (license license:gpl2+))))

(define-public r-kbet
  (let ((commit "f35171dfb04c7951b8a09ac778faf7424c4b6bc0")
        (revision "1"))
    (package
      (name "r-kbet")
      (version (git-version "0.99.6" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/theislab/kBET")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1r91prl2kki3zk694vhlmxdlqh0ixlhs8jfcqw6wc7cdsa0nv67k"))))
      (properties `((upstream-name . "kBET")))
      (build-system r-build-system)
      (propagated-inputs (list r-cluster r-fnn r-ggplot2 r-mass r-rcolorbrewer))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/theislab/kBET")
      (synopsis "k-nearest neighbour batch effect test")
      (description
       "This tool detects batch effects in high-dimensional data based on chi^2-test.")
      ;; Any version of the GPL
      (license license:gpl3+))))

(define-public python-vireosnp
  (package
    (name "python-vireosnp")
    (version "0.5.7")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "vireoSNP" version))
              (sha256
               (base32
                "02ybhzivsxwnb1axlgbs63wni1j27xajnkl4jw1ps5vmsz2l4b0d"))))
    (build-system python-build-system)
    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
    (home-page "https://github.com/huangyh09/vireoSNP")
    (synopsis "Deconvolution based on SNP for multiplexed scRNA-seq data")
    (description
     "This package provides a deconvolution based on Single Nucleotide
Position (SNP) for multiplexed scRNA-seq data.  The name vireo stand for
Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in
multiplexed scRNA-seq data and follows the clone identification from
single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.")
    (license license:asl2.0)))

(define-public ccwl
  (package
    (name "ccwl")
    (version "0.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://ccwl.systemreboot.net/releases/ccwl-"
                           version ".tar.lz"))
       (sha256
        (base32
         "0za710mcn9di1njli3dk3660n3836ip8b4msb8f958498va95y7j"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags '("GUILE_AUTO_COMPILE=0") ; to prevent guild warnings
       #:modules (((guix build guile-build-system)
                   #:select (target-guile-effective-version))
                  ,@%default-gnu-modules)
       #:imported-modules ((guix build guile-build-system)
                           ,@%default-gnu-imported-modules)
       #:phases
       (modify-phases %standard-phases
         (add-after 'patch-source-shebangs 'patch-more-source-shebangs
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "scripts/ccwl"
               (("^exec guile")
                (string-append "exec "
                               (search-input-file inputs "/bin/guile"))))))
         (add-after 'install 'wrap
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (effective-version (target-guile-effective-version)))
               (wrap-program (string-append out "/bin/ccwl")
                 `("GUILE_LOAD_PATH" prefix
                   (,(string-append out "/share/guile/site/" effective-version)
                    ,(getenv "GUILE_LOAD_PATH")))
                 `("GUILE_LOAD_COMPILED_PATH" prefix
                   (,(string-append out "/lib/guile/" effective-version "/site-ccache")
                    ,(getenv "GUILE_LOAD_COMPILED_PATH"))))))))))
    (inputs
     (list bash-minimal
           guile-3.0
           guile-libyaml))
    (native-inputs
     (list pkg-config
           lzip
           ;; To build documentation
           cwltool
           graphviz
           skribilo))
    (home-page "https://ccwl.systemreboot.net")
    (synopsis "Concise common workflow language")
    (description "The @acronym{ccwl, Concise Common Workflow Language} is a
concise syntax to express CWL workflows.  ccwl is a compiler to generate CWL
workflows from concise descriptions in ccwl.  It is implemented as an
@acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming
language.")
    (license license:gpl3+)))

(define-public hh-suite
  (package
    (name "hh-suite")
    (version "3.3.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/soedinglab/hh-suite")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1bcmzg0ii6nkda2xm5jdddbwkgsag7k38j20af0c9chr2mbxwx4d"))
       (modules '((guix build utils)))
       (snippet
        '(delete-file-recursively "lib/simde"))))
    (build-system cmake-build-system)
    (arguments '(#:tests? #false)) ;no test target
    (inputs
     (list openmpi simde))
    (native-inputs
     (list perl pkg-config xxd))
    (home-page "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7")
    (synopsis "Remote protein homology detection suite")
    (description "The HH-suite is a software package for sensitive protein sequence searching
based on the pairwise alignment of hidden Markov models (HMMs).")
    (license license:gpl3+)))

(define-public wfmash
  (package
    (name "wfmash")
    (version "0.21.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/waveygang/wfmash/releases/download/v"
                           version "/wfmash-v" version ".tar.gz"))
       (sha256
        (base32
         "0v9giqrqxl9kkcrs6zrfj1y07j6p9r8d82kkwigvndlg1708457w"))
       (snippet
        #~(begin
            (use-modules (guix build utils))
            ;; Unbundle atomic-queue.
            (delete-file-recursively "src/common/atomic_queue")
            (substitute* "src/align/include/computeAlignments.hpp"
              (("\"common/atomic_queue/atomic_queue.h\"")
               "<atomic_queue/atomic_queue.h>"))
            ;; Remove compiler optimizations.
            (substitute* (find-files "." "CMakeLists\\.txt")
              (("-march=native ") ""))))))
    (build-system cmake-build-system)
    (arguments
     (list
      ;; Tests time out on riscv64-linux.
      #:tests? (and (not (%current-target-system))
                    (not (target-riscv64?)))
      #:configure-flags
      #~(list "-DWFA_PNG_AND_TSV=ON")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-cmakelists
            (lambda _
              (substitute* "CMakeLists.txt"
                ;; Remove broken configure of CTestCustom.cmake.
                (("^configure_file[^\n]*") "")
                ;; Do not hard-code wfmash executable.
                (("\\./build/bin/wfmash") "wfmash"))))
          (add-before 'check 'build-check-prerequisites
            (lambda _
              (let ((wfa2-lib #$(string-append "../wfmash-v"
                                               version
                                               "/src/common/wflign/deps/WFA2-lib")))
                (substitute* (string-append wfa2-lib "/Makefile")
                  ;; Remove architecture-specific flags.
                  (("-march=x86-64-v3") ""))
                (substitute* (string-append wfa2-lib "/tests/wfa.utest.sh")
                  ;; Fix time command.
                  (("\\\\time -v") "time"))
                ;; Build wfa2-lib.
                (invoke "make" "-C" wfa2-lib
                        #$(string-append "CC=" (cc-for-target)))))))))
    (inputs
     (list atomic-queue
           gsl
           htslib
           libdeflate
           zlib))
    (native-inputs
     (list pkg-config
           samtools))
    (synopsis "Base-accurate DNA sequence aligner")
    (description "@code{wfmash} is a DNA sequence read mapper based on mash
distances and the wavefront alignment algorithm.  It is a fork of MashMap that
implements base-level alignment via the wflign tiled wavefront global
alignment algorithm.  It completes MashMap with a high-performance alignment
module capable of computing base-level alignments for very large sequences.")
    (home-page "https://github.com/waveygang/wfmash")
    (license license:expat)))

(define-public gdcm
  (package
    (name "gdcm")
    (version "3.0.20")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/malaterre/gdcm")
                    (commit (string-append "v" version))
                    (recursive? #t)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l"))))
    (build-system cmake-build-system)
    (outputs '("out" "doc"))
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'build 'set-HOME
            ;; The build spams ‘Fontconfig error: No writable cache
            ;; directories’ in a seemingly endless loop otherwise.
            (lambda _
              (setenv "HOME" "/tmp"))))
      #:configure-flags
      #~(list "-DGDCM_BUILD_TESTING=true"
              (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;"
                             "'TestFileMetaInformation"
                             "|TestElement2"
                             "|TestSCUValidation"
                             "|TestWriter"
                             "|TestAnonymizer4"
                             "|TestPrinter1"
                             "|TestEcho"
                             ;; The scanner tests depend on TestWriter output
                             "|TestStrictScanner1"
                             "|TestStrictScanner2_1"
                             "|TestStrictScanner2"
                             "|TestStrictScanner2_2"
                             "|TestFind'")
              "-DGDCM_DOCUMENTATION:BOOL=ON"
              "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF"
              (string-append "-DGDCM_INSTALL_DOC_DIR="
                             #$output:doc "/share/doc/" #$name))))
    (native-inputs (list docbook-xsl doxygen graphviz libxslt))
    (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page")
    (synopsis "Grassroots DICOM library")
    (description
     "Grassroots DICOM (GDCM) is an implementation of the DICOM standard
designed to be open source so that researchers may access clinical data
directly.  GDCM includes a file format definition and a network communications
protocol, both of which should be extended to provide a full set of tools for
a researcher or small medical imaging vendor to interface with an existing
medical database.")
    (license license:bsd-3)))

(define-public wiggletools
  (package
    (name "wiggletools")
    (version "1.2.11")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/Ensembl/WiggleTools/")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1g3qla4l1g583nzlgyww5jqxpq87ndpn9cmjls098bgqjyn5292q"))))
    (build-system gnu-build-system)
    (arguments
     (list
      ;; Tests require internet access
      #:tests? #false
      #:make-flags
      #~(list "Wiggletools"
              (string-append "CC=" #$(cc-for-target)))
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (replace 'install
            (lambda _
              (install-file "bin/wiggletools"
                            (string-append #$output "/bin")))))))
    (inputs
     (list curl ; XXX: needed by libbigwig
           htslib libbigwig gsl xz zlib))
    (home-page "https://github.com/Ensembl/WiggleTools/")
    (synopsis "Operations on the space of numerical functions defined on the genome")
    (description "The WiggleTools package allows genomewide data files to be
manipulated as numerical functions, equipped with all the standard functional
analysis operators (sum, product, product by a scalar, comparators), and
derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank
sum test, etc).")
    (license license:asl2.0)))

(define-public flair
  (package
    (name "flair")
    (version "1.6.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/BrooksLabUCSC/flair")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0jviacx6qx5rwgi3wvl7a8a8ml19r6cpngddivlk13f6g9072din"))))
    (build-system python-build-system)
    (arguments
     (list
      #:tests? #false ;there are none
      #:phases
      #~(modify-phases %standard-phases
          ;; TODO: implement as a feature of python-build-system (PEP-621,
          ;; PEP-631, PEP-660)
          (replace 'build
            (lambda _
              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
              ;; ZIP does not support timestamps before 1980.
              (setenv "SOURCE_DATE_EPOCH" "315532800")
              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
          (replace 'install
            (lambda _
              (apply invoke "pip" "--no-cache-dir" "--no-input"
                     "install" "--no-deps" "--prefix" #$output
                     (find-files "dist" "\\.whl$"))))
          (add-after 'install 'wrap-executable
            (lambda _
              (for-each
               (lambda (script)
                 (wrap-program script
                   `("R_HOME" ":" = (,(string-append #$r-minimal "/lib/R")))
                   `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
               (find-files (string-append #$output "/bin"))))))))
    (propagated-inputs
     (list python-mappy
           python-numpy
           python-ncls
           python-pybedtools
           python-pysam
           python-rpy2
           python-scipy
           python-tqdm))
    ;; Used by rpy2
    (inputs
     (list bash-minimal
           r-minimal  ;for R_LIBS_SITE
           r-apeglm   ;for runDE
           r-deseq2   ;for runDE
           r-drimseq  ;for runDS
           r-ggplot2  ;runDS, runDU
           r-lazyeval ;for rpy2
           r-qqman    ;for runDE
           r-rlang))  ;for rpy2
    (native-inputs
     (list python-pypa-build python-setuptools))
    (home-page "https://flair.readthedocs.io/en/latest/")
    (synopsis "Full-length alternative isoform analysis of RNA")
    (description "This package implements FLAIR (Full-Length Alternative
Isoform analysis of RNA) for the correction, isoform definition, and
alternative splicing analysis of noisy reads.  FLAIR has primarily been used
for nanopore cDNA, native RNA, and PacBio sequencing reads.")
    (license license:bsd-3)))

(define-public go-github-com-biogo-graph
  (package
    (name "go-github-com-biogo-graph")
    (version "0.0.0-20150317020928-057c1989faed")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biogo/graph")
                    (commit (go-version->git-ref version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1kpzs5dfd5dsk4mg1g2qjz1prqd84ixhrcxxnf90hq25vxcnk7lh"))))
    (build-system go-build-system)
    (arguments
     '(#:import-path "github.com/biogo/graph"
       #:tests? #false))      ;TODO: one of 13 tests fails for unknown reasons
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (home-page "https://github.com/biogo/graph")
    (synopsis "Undirected graph analysis for biogo")
    (description "The package @code{graph} implements graph manipulation
functions.")
    (license license:bsd-3)))

(define-public go-github-com-biogo-store-interval
  (package
    (name "go-github-com-biogo-store-interval")
    (version "0.0.0-20201120204734-aad293a2328f")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biogo/store")
                    (commit (go-version->git-ref version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0skizrp1j6vgbl0g1kmh73picagqlvwckaqs0gkl6rai5lckxj8a"))))
    (build-system go-build-system)
    (arguments
     '(#:import-path "github.com/biogo/store/interval"
       #:unpack-path "github.com/biogo/store"))
    (propagated-inputs
     (list go-gopkg-in-check-v1
           go-github-com-kr-pretty))
    (home-page "https://github.com/biogo/store")
    (synopsis "Interval store type for biogo")
    (description
     "The @code{store} package provides a number of data store types that are
useful for bioinformatic analysis.")
    (license license:bsd-3)))

(define-public go-github-com-biogo-store-kdtree
  (package
    (inherit go-github-com-biogo-store-interval)
    (name "go-github-com-biogo-store-kdtree")
    (arguments
     '(#:import-path "github.com/biogo/store/kdtree"
       #:unpack-path "github.com/biogo/store"))
    (propagated-inputs
     (list go-gopkg-in-check-v1
           go-github-com-kr-pretty))
    (synopsis "kdtree store type for biogo")))

(define-public go-github-com-biogo-store-llrb
  (package
    (inherit go-github-com-biogo-store-interval)
    (name "go-github-com-biogo-store-llrb")
    (arguments
     '(#:import-path "github.com/biogo/store/llrb"
       #:unpack-path "github.com/biogo/store"))
    (propagated-inputs
     (list go-gopkg-in-check-v1
           go-github-com-kr-pretty))
    (synopsis "LLRB store for biogo")))

(define-public go-github-com-biogo-store-step
  (package
    (inherit go-github-com-biogo-store-interval)
    (name "go-github-com-biogo-store-step")
    (arguments
     '(#:import-path "github.com/biogo/store/step"
       #:unpack-path "github.com/biogo/store"))
    (propagated-inputs
     (list go-gopkg-in-check-v1
           go-github-com-kr-pretty))
    (synopsis "Step store for biogo")))

(define-public go-github-com-biogo-hts-bam
  (package
    (name "go-github-com-biogo-hts-bam")
    (version "1.4.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biogo/hts")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1vkcqxyajghx5p5j7g2i376nbsxh8q2smk0smlv8mi34yr7hlw5b"))))
    (build-system go-build-system)
    (arguments
     '(#:import-path "github.com/biogo/hts/bam"
       #:unpack-path "github.com/biogo/hts"))
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (home-page "https://github.com/biogo/hts")
    (synopsis "HTS BAM module for biogo")
    (description "This package provides tools for handling BAM files.")
    (license license:bsd-3)))

(define-public go-github-com-biogo-hts-sam
  (package
    (inherit go-github-com-biogo-hts-bam)
    (name "go-github-com-biogo-hts-sam")
    (arguments
     '(#:import-path "github.com/biogo/hts/sam"
       #:unpack-path "github.com/biogo/hts"))
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (synopsis "HTS SAM module for biogo")
    (description "This package provides tools for handling SAM files.")))

(define-public go-github-com-biogo-hts-tabix
  (package
    (inherit go-github-com-biogo-hts-bam)
    (name "go-github-com-biogo-hts-tabix")
    (arguments
     '(#:import-path "github.com/biogo/hts/tabix"
       #:unpack-path "github.com/biogo/hts"))
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (synopsis "HTS Tabix module for biogo")
    (description "This package provides tools for handling Tabix files.")))

(define-public go-github-com-biogo-hts-bgzf
  (package
    (inherit go-github-com-biogo-hts-bam)
    (name "go-github-com-biogo-hts-bgzf")
    (arguments
     '(#:import-path "github.com/biogo/hts/bgzf"
       #:unpack-path "github.com/biogo/hts"))
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (synopsis "HTS bgzf module for biogo")
    (description "This package provides tools for handling bgzf files.")))

(define-public go-github-com-biogo-hts-cram
  (package
    (inherit go-github-com-biogo-hts-bam)
    (name "go-github-com-biogo-hts-cram")
    (arguments
     '(#:import-path "github.com/biogo/hts/cram"
       #:unpack-path "github.com/biogo/hts"
       #:tests? #false)) ;require network access
    (propagated-inputs
     (list go-gopkg-in-check-v1
           go-github-com-ulikunitz-xz
           go-github-com-kortschak-utter))
    (synopsis "HTS CRAM module for biogo")
    (description "This package provides tools for handling CRAM files.")))

(define-public go-github-com-biogo-hts-csi
  (package
    (inherit go-github-com-biogo-hts-bam)
    (name "go-github-com-biogo-hts-csi")
    (arguments
     '(#:import-path "github.com/biogo/hts/csi"
       #:unpack-path "github.com/biogo/hts"))
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (synopsis "Coordinate sorted indexing for biogo")
    (description "This package implements CSIv1 and CSIv2 coordinate sorted
indexing.")))

(define-public go-github-com-biogo-hts-fai
  (package
    (inherit go-github-com-biogo-hts-bam)
    (name "go-github-com-biogo-hts-fai")
    (arguments
     '(#:import-path "github.com/biogo/hts/fai"
       #:unpack-path "github.com/biogo/hts"))
    (propagated-inputs
     (list go-gopkg-in-check-v1))
    (synopsis "Fasta sequence file index handling for biogo")
    (description "This package implements FAI fasta sequence file index
handling.")))

(define-public go-github-com-biogo-biogo
  (package
    (name "go-github-com-biogo-biogo")
    (version "1.0.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/biogo/biogo")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0ali1mqf3dc26myv6l7wmqfr8i25461rbq3qdad8s0wi29622199"))))
    (build-system go-build-system)
    (arguments
     '(#:import-path "github.com/biogo/biogo"))
    (propagated-inputs
     (list go-gopkg-in-check-v1
           go-github-com-biogo-store-interval
           go-github-com-biogo-store-kdtree
           go-github-com-biogo-store-llrb
           go-github-com-biogo-store-step
           go-github-com-biogo-hts-bam
           go-github-com-biogo-graph))
    (home-page "https://github.com/biogo/biogo")
    (synopsis "Bioinformatics library for Go")
    (description
     "Bíogo is a bioinformatics library for the Go language.")
    (license license:bsd-3)))

(define-public python-gseapy
  (package
    (name "python-gseapy")
    (version "1.0.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/zqfang/GSEApy")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "06gh09dwwj2xr5zx8i41smy8arx2pw7rll7sk50np28z419bnyz9"))))
    (build-system cargo-build-system)
    (arguments
     (list
      #:install-source? #false
      #:features '(list "extension-module")
      #:cargo-test-flags '(list "--features=extension-module")
      #:cargo-inputs
      `(("rust-csv" ,rust-csv-1)
        ("rust-itertools" ,rust-itertools-0.10)
        ("rust-pyo3" ,rust-pyo3-0.16)
        ("rust-rand" ,rust-rand-0.8)
        ("rust-rayon" ,rust-rayon-1)
        ("rust-serde" ,rust-serde-1))
      #:imported-modules
      (append %cargo-build-system-modules
              %pyproject-build-system-modules)
      #:modules
      '((guix build cargo-build-system)
        ((guix build pyproject-build-system) #:prefix py:)
        (guix build utils))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'install 'prepare-python-module
            (lambda _
              ;; We don't use maturin, nor do we use setuptools-rust.
              (delete-file "pyproject.toml")
              (call-with-output-file "pyproject.toml"
                (lambda (port)
                  (format port "\
[build-system]
build-backend = 'setuptools.build_meta'
requires = ['setuptools']
")))
              (delete-file "setup.py")
              (call-with-output-file "setup.cfg"
                (lambda (port)
                  (format port "\
[metadata]
name = gseapy
version = ~a

[options]
packages = find:

[options.packages.find]
exclude =
  src
  docs
  tests
  Cargo.toml
" #$version)))))
          ;; We delete the Cargo checks but run the Python tests later.
          ;; See https://github.com/zqfang/GSEApy/issues/207
          (delete 'check)
          (add-after 'prepare-python-module 'enable-bytecode-determinism
            (assoc-ref py:%standard-phases 'enable-bytecode-determinism))
          (add-after 'enable-bytecode-determinism 'build-python-module
            (assoc-ref py:%standard-phases 'build))
          (add-after 'build-python-module 'install-python-module
            (assoc-ref py:%standard-phases 'install))
          (add-after 'install-python-module 'install-python-library
            (lambda _
              (let ((site (string-append #$output "/lib/python"
                                         #$(version-major+minor
                                            (package-version python))
                                         "/site-packages")))
                (mkdir-p site)
                (copy-file "target/release/libgse.so"
                           (string-append site "/gseapy/gse.so")))))
          (add-after 'install-python-library 'add-install-to-pythonpath
            (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
          (add-after 'add-install-to-pythonpath 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (invoke "pytest" "-vv" "tests"
                        ;; These tests need access to the internet
                        "-k" "not test_enrichr and not test_prerank")))))))
    (inputs
     (list python-wrapper))
    (native-inputs
     (list python-pytest))
    (propagated-inputs
     (list python-numpy
           python-scipy
           python-pandas
           python-matplotlib
           python-requests))
    (home-page "https://github.com/zqfang/gseapy")
    (synopsis "Gene Set Enrichment Analysis in Python")
    (description "GSEApy is a Python/Rust implementation for GSEA and wrapper
for Enrichr.  GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It
can be used for convenient GO enrichment and to produce publication quality
figures in Python.")
    (license license:bsd-3)))

;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above by existing packages with similar
;;; functionality or similar names.
;;;

debug log:

solving f84306b6b9 ...
found f84306b6b9 in https://git.savannah.gnu.org/cgit/guix.git

(*) Git path names are given by the tree(s) the blob belongs to.
    Blobs themselves have no identifier aside from the hash of its contents.^
Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/guix.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).