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* [PATCH] Add python–plastid, python-twobitreader.
@ 2016-04-06 14:36 Ricardo Wurmus
  2016-04-06 19:11 ` Leo Famulari
  0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2016-04-06 14:36 UTC (permalink / raw)
  To: guix-devel

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
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From ecb23f8eb2dbd83cbaa97972d6258ccb44c58194 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 6 Apr 2016 16:34:19 +0200
Subject: [PATCH 1/2] gnu: Add python-twobitreader.

* gnu/packages/bioinformatics.scm (python-twobitreader,
  python2-twobitreader): New variables.
---
 gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 01e9060..d13303d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1038,6 +1038,29 @@ also includes an interface for tabix.")
 (define-public python2-pysam
   (package-with-python2 python-pysam))
 
+(define-public python-twobitreader
+  (package
+    (name "python-twobitreader")
+    (version "3.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "twobitreader" version))
+              (sha256
+               (base32
+                "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-sphinx" ,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 python2-twobitreader
+  (package-with-python2 python-twobitreader))
+
 (define-public cd-hit
   (package
     (name "cd-hit")
-- 
2.1.0


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From a2604f6d4b03727ebd7922ce373486b13ab31c00 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 6 Apr 2016 16:35:09 +0200
Subject: [PATCH 2/2] gnu: Add python-plastid.

* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
  variables.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d13303d..1896002 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1061,6 +1061,41 @@ UCSC genome browser.")
 (define-public python2-twobitreader
   (package-with-python2 python-twobitreader))
 
+(define-public python-plastid
+  (package
+    (name "python-plastid")
+    (version "0.4.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "plastid" version))
+              (sha256
+               (base32
+                "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
+    (build-system python-build-system)
+    (arguments
+     ;; Some test files are not included.
+     `(#:tests? #f))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-pandas" ,python-pandas)
+       ("python-pysam" ,python-pysam)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-biopython" ,python-biopython)
+       ("python-twobitreader" ,python-twobitreader)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-nose" ,python-nose)))
+    (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 python2-plastid
+  (package-with-python2 python-plastid))
+
 (define-public cd-hit
   (package
     (name "cd-hit")
-- 
2.1.0


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2016-04-06 14:36 [PATCH] Add python–plastid, python-twobitreader Ricardo Wurmus
2016-04-06 19:11 ` Leo Famulari

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