85 lines
3.2 KiB
Scheme
85 lines
3.2 KiB
Scheme
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages bioinformatics)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix build-system gnu)
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#:use-module (gnu packages)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python))
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(define-public samtools
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(package
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(name "samtools")
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(version "1.1")
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(source
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(origin
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(method url-fetch)
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(uri
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(string-append "mirror://sourceforge/samtools/"
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version "/samtools-" version ".tar.bz2"))
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(sha256
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(base32
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"1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
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(build-system gnu-build-system)
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(arguments
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'(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
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#:phases
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(alist-cons-after
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'unpack
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'patch-makefile-curses
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(lambda _
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(substitute* "Makefile"
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(("-lcurses") "-lncurses")))
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(alist-cons-after
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'unpack
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'patch-tests
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((bash (assoc-ref inputs "bash")))
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(substitute* "test/test.pl"
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;; The test script calls out to /bin/bash
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(("/bin/bash")
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(string-append bash "/bin/bash"))
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;; There are two failing tests upstream relating to the "stats"
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;; subcommand in test_usage_subcommand ("did not have Usage"
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;; and "usage did not mention samtools stats"), so we disable
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;; them.
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(("(test_usage_subcommand\\(.*\\);)" cmd)
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(string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
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(alist-delete
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'configure
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%standard-phases)))))
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(native-inputs `(("pkg-config" ,pkg-config)))
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(inputs `(("ncurses" ,ncurses)
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("perl" ,perl)
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("python" ,python)
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("zlib" ,zlib)))
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(home-page "http://samtools.sourceforge.net")
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(synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
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(description
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"Samtools implements various utilities for post-processing nucleotide
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sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
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variant calling (in conjunction with bcftools), and a simple alignment
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viewer.")
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(license license:expat)))
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