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| | ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; 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 download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
#:use-module (gnu packages compression)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python))
(define-public bedtools
(package
(name "bedtools")
(version "2.22.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
version ".tar.gz"))
(sha256
(base32
"16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
(build-system gnu-build-system)
(inputs `(("python" ,python)
("samtools" ,samtools)
("zlib" ,zlib)))
(arguments
'(#:test-target "test"
#:phases
(alist-cons-after
'unpack 'patch-makefile-SHELL-definition
(lambda _
;; patch-makefile-SHELL cannot be used here as it does not
;; yet patch definitions with `:='. Since changes to
;; patch-makefile-SHELL result in a full rebuild, features
;; of patch-makefile-SHELL are reimplemented here.
(define (find-shell name)
(let ((shell
(search-path (search-path-as-string->list (getenv "PATH"))
name)))
(unless shell
(format (current-error-port)
"patch-makefile-SHELL: warning: no binary for shell `~a' found in $PATH~%"
name))
shell))
(substitute* "Makefile"
(("^SHELL := .*$") (string-append "SHELL := " (find-shell "bash") " -e \n"))))
(alist-delete
'configure
(alist-replace
'install (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(tools
'("bamToFastq" "mapBed" "shuffleBed" "bed12ToBed6" "bedToBam"
"multiIntersectBed" "complementBed" "randomBed" "tagBam" "sortBed"
"annotateBed" "clusterBed" "fastaFromBed" "coverageBed" "bedpeToBam"
"pairToPair" "subtractBed" "nucBed" "expandCols" "bedToIgv" "slopBed"
"closestBed" "windowMaker" "linksBed" "getOverlap" "mergeBed" "windowBed"
"flankBed" "pairToBed" "intersectBed" "bamToBed" "multiBamCov"
"unionBedGraphs" "genomeCoverageBed" "groupBy" "maskFastaFromBed"
"bedtools")))
(mkdir-p bin)
(map (lambda (tool)
(copy-file (string-append "bin/" tool)
(string-append bin "/" tool)))
tools)))
%standard-phases)))))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Swiss army knife for genome 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:gpl2)))
(define-public samtools
(package
(name "samtools")
(version "1.1")
(source
(origin
(method url-fetch)
(uri
(string-append "mirror://sourceforge/samtools/"
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
"1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(alist-cons-after
'unpack
'patch-makefile-curses
(lambda _
(substitute* "Makefile"
(("-lcurses") "-lncurses")))
(alist-cons-after
'unpack
'patch-tests
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash (assoc-ref inputs "bash")))
(substitute* "test/test.pl"
;; The test script calls out to /bin/bash
(("/bin/bash")
(string-append bash "/bin/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 "};")))))
(alist-delete
'configure
%standard-phases)))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses)
("perl" ,perl)
("python" ,python)
("zlib" ,zlib)))
(home-page "http://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)))
|