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gnu: Add samtools

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* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
This commit is contained in:
Ricardo Wurmus 2014-12-11 15:48:22 +01:00 committed by Ludovic Courtès
parent 97ab2c0fb6
commit 4e10a22168
2 changed files with 85 additions and 0 deletions
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1
gnu-system.am
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@ -45,6 +45,7 @@ GNU_SYSTEM_MODULES = \
gnu/packages/base.scm \
gnu/packages/bash.scm \
gnu/packages/bdw-gc.scm \
gnu/packages/bioinformatics.scm \
gnu/packages/bittorrent.scm \
gnu/packages/bison.scm \
gnu/packages/boost.scm \

84
gnu/packages/bioinformatics.scm Normal file
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@ -0,0 +1,84 @@
;;; 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 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)))