mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-11-08 16:06:16 -05:00
85 lines
3.2 KiB
Scheme
85 lines
3.2 KiB
Scheme
|
;;; 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)))
|