533 lines
22 KiB
Scheme
533 lines
22 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2014, 2015 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 (guix build-system cmake)
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#:use-module (guix build-system python)
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#:use-module (guix build-system trivial)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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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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#:use-module (gnu packages tbb)
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#:use-module (gnu packages vim)
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#:use-module (gnu packages zip))
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(define-public bedops
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(package
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(name "bedops")
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(version "2.4.5")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/bedops/bedops/archive/v"
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version ".tar.gz"))
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(sha256
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(base32
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"0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5"))))
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(build-system gnu-build-system)
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(arguments
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'(#:tests? #f
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#:make-flags (list (string-append "BINDIR=" %output "/bin"))
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#:phases
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(alist-cons-after
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'unpack 'unpack-tarballs
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(lambda _
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;; FIXME: Bedops includes tarballs of minimally patched upstream
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;; libraries jansson, zlib, and bzip2. We cannot just use stock
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;; libraries because at least one of the libraries (zlib) is
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;; patched to add a C++ function definition (deflateInit2cpp).
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;; Until the Bedops developers offer a way to link against system
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;; libraries we have to build the in-tree copies of these three
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;; libraries.
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;; See upstream discussion:
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;; https://github.com/bedops/bedops/issues/124
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;; Unpack the tarballs to benefit from shebang patching.
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(with-directory-excursion "third-party"
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(and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
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(zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
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(zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
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;; Disable unpacking of tarballs in Makefile.
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(substitute* "system.mk/Makefile.linux"
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(("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
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(("\\./configure") "CONFIG_SHELL=bash ./configure"))
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(substitute* "third-party/zlib-1.2.7/Makefile.in"
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(("^SHELL=.*$") "SHELL=bash\n")))
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(alist-delete 'configure %standard-phases))))
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(home-page "https://github.com/bedops/bedops")
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(synopsis "Tools for high-performance genomic feature operations")
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(description
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"BEDOPS is a suite of tools to address common questions raised in genomic
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studies---mostly with regard to overlap and proximity relationships between
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data sets. It aims to be scalable and flexible, facilitating the efficient
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and accurate analysis and management of large-scale genomic data.
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BEDOPS provides tools that perform highly efficient and scalable Boolean and
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other set operations, statistical calculations, archiving, conversion and
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other management of genomic data of arbitrary scale. Tasks can be easily
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split by chromosome for distributing whole-genome analyses across a
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computational cluster.")
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(license license:gpl2+)))
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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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(patches (list (search-patch "bowtie-fix-makefile.patch")))))
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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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(supported-systems '("x86_64-linux"))
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(license license:gpl3+)))
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(define-public flexbar
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(package
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(name "flexbar")
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(version "2.5")
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(source (origin
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(method url-fetch)
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(uri
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(string-append "mirror://sourceforge/flexbar/"
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version "/flexbar_v" version "_src.tgz"))
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(sha256
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(base32
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"13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
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(build-system cmake-build-system)
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(arguments
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`(;; There is no test target, although there is a directory containing
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;; test data and scripts (launched by flexbar_validate.sh).
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#:tests? #f
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#:configure-flags (list
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(string-append "-DFLEXBAR_BINARY_DIR="
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(assoc-ref %outputs "out")
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"/bin/"))
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#:phases
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(alist-delete 'install %standard-phases)))
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(inputs
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`(("tbb" ,tbb)
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("zlib" ,zlib)))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("seqan" ,seqan)))
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(home-page "http://flexbar.sourceforge.net")
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(synopsis "Barcode and adapter removal tool for sequencing platforms")
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(description
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"Flexbar preprocesses high-throughput nucleotide sequencing data
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efficiently. It demultiplexes barcoded runs and removes adapter sequences.
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Moreover, trimming and filtering features are provided. Flexbar increases
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read mapping rates and improves genome and transcriptome assemblies. It
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supports next-generation sequencing data in fasta/q and csfasta/q format from
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Illumina, Roche 454, and the SOLiD platform.")
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(license license:gpl3)))
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(define-public hisat
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(package
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(name "hisat")
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(version "0.1.4")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://ccb.jhu.edu/software/hisat/downloads/hisat-"
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version "-beta-source.zip"))
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(sha256
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(base32
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"1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no check target
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#:make-flags '("allall"
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;; Disable unsupported `popcnt' instructions on
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;; architectures other than x86_64
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,@(if (string-prefix? "x86_64"
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(or (%current-target-system)
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(%current-system)))
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'()
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'("POPCNT_CAPABILITY=0")))
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#:phases
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(alist-replace
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'unpack
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(lambda* (#:key source #:allow-other-keys)
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(and (zero? (system* "unzip" source))
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(chdir "hisat-0.1.4-beta")))
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(alist-cons-after
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'unpack 'patch-sources
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(lambda _
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;; XXX Cannot use snippet because zip files are not supported
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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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(substitute* '("hisat-build" "hisat-inspect")
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(("/usr/bin/env") (which "env"))))
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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
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(lambda (file)
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(copy-file file (string-append bin file)))
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(find-files
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"."
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"hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
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(alist-delete 'configure %standard-phases))))))
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(native-inputs
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`(("unzip" ,unzip)))
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(inputs
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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://ccb.jhu.edu/software/hisat/index.shtml")
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(synopsis "Hierarchical indexing for spliced alignment of transcripts")
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(description
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"HISAT is a fast and sensitive spliced alignment program for mapping
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RNA-seq reads. In addition to one global FM index that represents a whole
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genome, HISAT uses a large set of small FM indexes that collectively cover the
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whole genome. These small indexes (called local indexes) combined with
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several alignment strategies enable effective alignment of RNA-seq reads, in
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particular, reads spanning multiple exons.")
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(license license:gpl3+)))
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(define-public htseq
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(package
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(name "htseq")
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(version "0.6.1")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
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version ".tar.gz"))
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(sha256
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(base32
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"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
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(build-system python-build-system)
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(arguments `(#:python ,python-2)) ; only Python 2 is supported
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(inputs
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`(("python-numpy" ,python2-numpy)
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("python-setuptools" ,python2-setuptools)))
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(home-page "http://www-huber.embl.de/users/anders/HTSeq/")
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(synopsis "Analysing high-throughput sequencing data with Python")
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(description
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"HTSeq is a Python package that provides infrastructure to process data
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from high-throughput sequencing assays.")
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(license license:gpl3+)))
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(define-public rseqc
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(package
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(name "rseqc")
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(version "2.6.1")
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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/rseqc/"
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version "/RSeQC-" version ".tar.gz"))
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(sha256
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(base32 "09rf0x9d6apjja5l01cgprj7vigpw6kiqhy34ibwwlxil0db0ri4"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; remove bundled copy of pysam
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(delete-file-recursively "lib/pysam")
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(substitute* "setup.py"
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;; remove dependency on outdated "distribute" module
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(("^from distribute_setup import use_setuptools") "")
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(("^use_setuptools\\(\\)") "")
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;; do not use bundled copy of pysam
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(("^have_pysam = False") "have_pysam = True"))))))
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(build-system python-build-system)
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(arguments `(#:python ,python-2))
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(inputs
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`(("python-cython" ,python2-cython)
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("python-pysam" ,python2-pysam)
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("python-numpy" ,python2-numpy)
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|
("python-setuptools" ,python2-setuptools)
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|
("zlib" ,zlib)))
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(native-inputs
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`(("python-nose" ,python2-nose)))
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(home-page "http://rseqc.sourceforge.net/")
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(synopsis "RNA-seq quality control package")
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(description
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"RSeQC provides a number of modules that can comprehensively evaluate
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high throughput sequence data, especially RNA-seq data. Some basic modules
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inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
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while RNA-seq specific modules evaluate sequencing saturation, mapped reads
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distribution, coverage uniformity, strand specificity, etc.")
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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"))
|
|
(sha256
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|
(base32
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|
"1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
|
|
(build-system gnu-build-system)
|
|
(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
|
|
'patch-makefile-curses
|
|
(lambda _
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|
(substitute* "Makefile"
|
|
(("-lcurses") "-lncurses")))
|
|
(alist-cons-after
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|
'unpack
|
|
'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)))
|
|
(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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|
|
(define-public seqan
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(package
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(name "seqan")
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(version "1.4.2")
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(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://packages.seqan.de/seqan-library/"
|
|
"seqan-library-" version ".tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
|
|
;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
|
|
;; makes sense to split the outputs.
|
|
(outputs '("out" "doc"))
|
|
(build-system trivial-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils))
|
|
#:builder
|
|
(begin
|
|
(use-modules (guix build utils))
|
|
(let ((tar (assoc-ref %build-inputs "tar"))
|
|
(bzip (assoc-ref %build-inputs "bzip2"))
|
|
(out (assoc-ref %outputs "out"))
|
|
(doc (assoc-ref %outputs "doc")))
|
|
(setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
|
|
(system* "tar" "xvf" (assoc-ref %build-inputs "source"))
|
|
(chdir (string-append "seqan-library-" ,version))
|
|
(copy-recursively "include" (string-append out "/include"))
|
|
(copy-recursively "share" (string-append doc "/share"))))))
|
|
(native-inputs
|
|
`(("source" ,source)
|
|
("tar" ,tar)
|
|
("bzip2" ,bzip2)))
|
|
(home-page "http://www.seqan.de")
|
|
(synopsis "Library for nucleotide sequence analysis")
|
|
(description
|
|
"SeqAn is a C++ library of efficient algorithms and data structures for
|
|
the analysis of sequences with the focus on biological data. It contains
|
|
algorithms and data structures for string representation and their
|
|
manipulation, online and indexed string search, efficient I/O of
|
|
bioinformatics file formats, sequence alignment, and more.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public star
|
|
(package
|
|
(name "star")
|
|
(version "2.4.0j")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://github.com/alexdobin/STAR/archive/STAR_"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1y3bciych1aw6s7k8sy1saj23dcan9wk4d4f96an499slkxwz712"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(substitute* "source/Makefile"
|
|
(("/bin/rm") "rm")))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
'(#:tests? #f ;no check target
|
|
#:make-flags '("STAR")
|
|
#:phases
|
|
(alist-cons-after
|
|
'unpack 'enter-source-dir (lambda _ (chdir "source"))
|
|
(alist-replace
|
|
'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
(mkdir-p bin)
|
|
(copy-file "STAR" (string-append bin "STAR"))))
|
|
(alist-delete
|
|
'configure %standard-phases)))))
|
|
(native-inputs
|
|
`(("vim" ,vim))) ; for xxd
|
|
(inputs
|
|
`(("zlib" ,zlib)))
|
|
(home-page "https://github.com/alexdobin/STAR")
|
|
(synopsis "Universal RNA-seq aligner")
|
|
(description
|
|
"The Spliced Transcripts Alignment to a Reference (STAR) software is
|
|
based on a previously undescribed RNA-seq alignment algorithm that uses
|
|
sequential maximum mappable seed search in uncompressed suffix arrays followed
|
|
by seed clustering and stitching procedure. In addition to unbiased de novo
|
|
detection of canonical junctions, STAR can discover non-canonical splices and
|
|
chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
|
|
sequences.")
|
|
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
|
|
(license license:gpl3+)))
|