199 lines
8.1 KiB
Scheme
199 lines
8.1 KiB
Scheme
;;; 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 bedtools
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(package
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(name "bedtools")
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(version "2.22.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
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version ".tar.gz"))
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(sha256
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(base32
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"16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
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(build-system gnu-build-system)
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(native-inputs `(("python" ,python-2)))
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(inputs `(("samtools" ,samtools)
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("zlib" ,zlib)))
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(arguments
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'(#:test-target "test"
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#:phases
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(alist-cons-after
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'unpack 'patch-makefile-SHELL-definition
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(lambda _
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;; patch-makefile-SHELL cannot be used here as it does not
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;; yet patch definitions with `:='. Since changes to
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;; patch-makefile-SHELL result in a full rebuild, features
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;; of patch-makefile-SHELL are reimplemented here.
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(substitute* "Makefile"
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(("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n"))))
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(alist-delete
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'configure
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(alist-replace
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'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
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(mkdir-p bin)
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(for-each (lambda (file)
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(copy-file file (string-append bin (basename file))))
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(find-files "bin" ".*"))))
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%standard-phases)))))
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(home-page "https://github.com/arq5x/bedtools2")
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(synopsis "Tools for genome analysis and arithmetic")
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(description
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"Collectively, the bedtools utilities are a swiss-army knife of tools for
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a wide-range of genomics analysis tasks. The most widely-used tools enable
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genome arithmetic: that is, set theory on the genome. For example, bedtools
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allows one to intersect, merge, count, complement, and shuffle genomic
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intervals from multiple files in widely-used genomic file formats such as BAM,
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BED, GFF/GTF, VCF.")
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(license license:gpl2)))
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(define-public bowtie
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(package
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(name "bowtie")
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(version "2.2.4")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
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version ".tar.gz"))
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(sha256
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(base32
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"15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
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(modules '((guix build utils)))
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(snippet
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'(substitute* "Makefile"
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(("^CC = .*$") "CC = gcc")
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(("^CPP = .*$") "CPP = g++")
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;; replace BUILD_HOST and BUILD_TIME for deterministic build
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(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
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(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
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(build-system gnu-build-system)
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(inputs `(("perl" ,perl)
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("perl-clone" ,perl-clone)
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("perl-test-deep" ,perl-test-deep)
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("perl-test-simple" ,perl-test-simple)
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("python" ,python-2)))
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(arguments
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'(#:make-flags '("allall")
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#:phases
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(alist-delete
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'configure
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(alist-replace
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'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
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(mkdir-p bin)
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(for-each (lambda (file)
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(copy-file file (string-append bin file)))
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(find-files "." "bowtie2.*"))))
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(alist-replace
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'check
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(lambda* (#:key outputs #:allow-other-keys)
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(system* "perl"
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"scripts/test/simple_tests.pl"
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"--bowtie2=./bowtie2"
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"--bowtie2-build=./bowtie2-build"))
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%standard-phases)))))
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(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
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(synopsis "Fast and sensitive nucleotide sequence read aligner")
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(description
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"Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
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reads to long reference sequences. It is particularly good at aligning reads
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of about 50 up to 100s or 1,000s of characters, and particularly good at
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aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
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genome with an FM Index to keep its memory footprint small: for the human
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genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
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gapped, local, and paired-end alignment modes.")
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(license license:gpl3+)))
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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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`(;; There are 87 test failures when building on non-64-bit architectures
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;; due to invalid test data. This has since been fixed upstream (see
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;; <https://github.com/samtools/samtools/pull/307>), but as there has
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;; not been a new release we disable the tests for all non-64-bit
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;; systems.
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#:tests? ,(string=? (or (%current-system) (%current-target-system))
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"x86_64-linux")
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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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