2014-12-11 14:48:22 +00:00
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;;; GNU Guix --- Functional package management for GNU
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2015-01-29 09:35:52 +00:00
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;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
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2015-06-17 09:21:22 +00:00
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;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
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2014-12-11 14:48:22 +00:00
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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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2015-03-20 15:17:55 +00:00
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#:use-module (guix utils)
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2014-12-11 14:48:22 +00:00
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#:use-module (guix download)
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2015-03-20 13:36:38 +00:00
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#:use-module (guix git-download)
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2014-12-11 14:48:22 +00:00
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#:use-module (guix build-system gnu)
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2015-02-06 14:42:02 +00:00
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#:use-module (guix build-system cmake)
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2015-05-27 13:14:19 +00:00
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#:use-module (guix build-system perl)
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2015-02-18 14:00:04 +00:00
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#:use-module (guix build-system python)
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2015-02-06 11:38:40 +00:00
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#:use-module (guix build-system trivial)
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2014-12-11 14:48:22 +00:00
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#:use-module (gnu packages)
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2015-06-17 09:21:22 +00:00
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#:use-module (gnu packages algebra)
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2015-02-06 11:38:40 +00:00
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#:use-module (gnu packages base)
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2015-04-16 13:18:10 +00:00
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#:use-module (gnu packages boost)
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2014-12-11 14:48:22 +00:00
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#:use-module (gnu packages compression)
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2015-06-16 14:24:24 +00:00
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#:use-module (gnu packages cpio)
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2015-04-14 12:42:49 +00:00
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#:use-module (gnu packages file)
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2015-03-05 09:24:12 +00:00
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#:use-module (gnu packages java)
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2015-04-14 12:43:32 +00:00
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#:use-module (gnu packages linux)
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2015-06-03 10:56:16 +00:00
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#:use-module (gnu packages machine-learning)
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2015-03-18 16:59:20 +00:00
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#:use-module (gnu packages maths)
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2014-12-11 14:48:22 +00:00
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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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2015-03-27 09:09:10 +00:00
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#:use-module (gnu packages popt)
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2015-04-16 13:18:10 +00:00
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#:use-module (gnu packages protobuf)
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2015-02-09 11:13:26 +00:00
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#:use-module (gnu packages python)
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2015-03-18 16:59:20 +00:00
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#:use-module (gnu packages statistics)
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2015-02-06 14:42:02 +00:00
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#:use-module (gnu packages tbb)
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2015-04-14 14:36:30 +00:00
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#:use-module (gnu packages textutils)
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2015-02-09 14:38:30 +00:00
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#:use-module (gnu packages vim)
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2015-05-27 13:14:19 +00:00
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#:use-module (gnu packages web)
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2015-03-18 16:59:20 +00:00
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#:use-module (gnu packages xml)
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2015-06-03 15:44:20 +00:00
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#:use-module (gnu packages zip)
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#:use-module (srfi srfi-1))
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2014-12-11 14:48:22 +00:00
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2015-07-21 14:37:23 +00:00
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(define-public aragorn
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(package
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(name "aragorn")
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(version "1.2.36")
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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://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
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version ".tgz"))
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(sha256
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(base32
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"1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; there are no tests
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(replace 'build
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(lambda _
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(zero? (system* "gcc"
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"-O3"
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"-ffast-math"
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"-finline-functions"
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"-o"
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"aragorn"
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(string-append "aragorn" ,version ".c")))))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(man (string-append out "/share/man/man1")))
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(mkdir-p bin)
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(copy-file "aragorn"
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(string-append bin "/aragorn"))
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(mkdir-p man)
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(copy-file "aragorn.1"
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(string-append man "/aragorn.1")))
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#t)))))
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(home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
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(synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
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(description
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"Aragorn identifies transfer RNA, mitochondrial RNA and
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transfer-messenger RNA from nucleotide sequences, based on homology to known
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tRNA consensus sequences and RNA structure. It also outputs the secondary
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structure of the predicted RNA.")
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(license license:gpl2)))
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2015-04-16 13:16:57 +00:00
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(define-public bamtools
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(package
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(name "bamtools")
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(version "2.3.0")
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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://github.com/pezmaster31/bamtools/archive/v"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
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(build-system cmake-build-system)
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2015-05-04 09:27:39 +00:00
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(arguments
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`(#:tests? #f ;no "check" target
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#:phases
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(modify-phases %standard-phases
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(add-before
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'configure 'set-ldflags
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(lambda* (#:key outputs #:allow-other-keys)
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(setenv "LDFLAGS"
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(string-append
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"-Wl,-rpath="
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(assoc-ref outputs "out") "/lib/bamtools")))))))
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2015-04-16 13:16:57 +00:00
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(inputs `(("zlib" ,zlib)))
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(home-page "https://github.com/pezmaster31/bamtools")
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(synopsis "C++ API and command-line toolkit for working with BAM data")
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(description
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"BamTools provides both a C++ API and a command-line toolkit for handling
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BAM files.")
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(license license:expat)))
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2015-02-11 15:55:33 +00:00
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(define-public bedops
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(package
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(name "bedops")
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2015-06-17 12:36:32 +00:00
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(version "2.4.14")
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2015-02-11 15:55:33 +00:00
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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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gnu: Add 'file-name' fields for github source tarballs without a name.
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-27 17:23:27 +00:00
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(file-name (string-append name "-" version ".tar.gz"))
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2015-02-11 15:55:33 +00:00
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(sha256
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(base32
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2015-06-17 12:36:32 +00:00
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"1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
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2015-02-11 15:55:33 +00:00
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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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2014-12-11 16:37:16 +00:00
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(define-public bedtools
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(package
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(name "bedtools")
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2015-07-24 13:11:31 +00:00
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(version "2.24.0")
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2014-12-11 16:37:16 +00:00
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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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gnu: Add 'file-name' fields for github source tarballs without a name.
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-27 17:23:27 +00:00
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(file-name (string-append name "-" version ".tar.gz"))
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2014-12-11 16:37:16 +00:00
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(sha256
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(base32
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2015-07-25 13:32:55 +00:00
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"0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
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(patches (list (search-patch "bedtools-32bit-compilation.patch")))))
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2014-12-11 16:37:16 +00:00
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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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(for-each (lambda (file)
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gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
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(install-file file bin))
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2014-12-11 16:37:16 +00:00
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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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2015-02-20 16:43:08 +00:00
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(define-public python2-pybedtools
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(package
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(name "python2-pybedtools")
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(version "0.6.9")
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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/p/pybedtools/pybedtools-"
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version ".tar.gz"))
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|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments `(#:python ,python-2)) ; no Python 3 support
|
|
|
|
(inputs
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
("python-matplotlib" ,python2-matplotlib)))
|
|
|
|
(propagated-inputs
|
|
|
|
`(("bedtools" ,bedtools)
|
|
|
|
("samtools" ,samtools)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-pyyaml" ,python2-pyyaml)
|
|
|
|
("python-nose" ,python2-nose)
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "https://pythonhosted.org/pybedtools/")
|
|
|
|
(synopsis "Python wrapper for BEDtools programs")
|
|
|
|
(description
|
|
|
|
"pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
|
|
|
|
which are widely used for genomic interval manipulation or \"genome algebra\".
|
|
|
|
pybedtools extends BEDTools by offering feature-level manipulations from with
|
|
|
|
Python.")
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
2015-06-03 15:44:20 +00:00
|
|
|
(define-public bioperl-minimal
|
|
|
|
(let* ((inputs `(("perl-module-build" ,perl-module-build)
|
|
|
|
("perl-data-stag" ,perl-data-stag)
|
|
|
|
("perl-libwww" ,perl-libwww)
|
|
|
|
("perl-uri" ,perl-uri)))
|
|
|
|
(transitive-inputs
|
|
|
|
(map (compose package-name cadr)
|
|
|
|
(delete-duplicates
|
|
|
|
(concatenate
|
|
|
|
(map (compose package-transitive-target-inputs cadr) inputs))))))
|
|
|
|
(package
|
|
|
|
(name "bioperl-minimal")
|
|
|
|
(version "1.6.924")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
|
|
|
|
(build-system perl-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after
|
|
|
|
'install 'wrap-programs
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
;; Make sure all executables in "bin" find the required Perl
|
|
|
|
;; modules at runtime. As the PERL5LIB variable contains also
|
|
|
|
;; the paths of native inputs, we pick the transitive target
|
|
|
|
;; inputs from %build-inputs.
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
(bin (string-append out "/bin/"))
|
|
|
|
(path (string-join
|
|
|
|
(cons (string-append out "/lib/perl5/site_perl")
|
|
|
|
(map (lambda (name)
|
|
|
|
(assoc-ref %build-inputs name))
|
|
|
|
',transitive-inputs))
|
|
|
|
":")))
|
|
|
|
(for-each (lambda (file)
|
|
|
|
(wrap-program file
|
|
|
|
`("PERL5LIB" ":" prefix (,path))))
|
|
|
|
(find-files bin "\\.pl$"))
|
|
|
|
#t))))))
|
|
|
|
(inputs inputs)
|
|
|
|
(native-inputs
|
|
|
|
`(("perl-test-most" ,perl-test-most)))
|
|
|
|
(home-page "http://search.cpan.org/dist/BioPerl")
|
|
|
|
(synopsis "Bioinformatics toolkit")
|
|
|
|
(description
|
|
|
|
"BioPerl is the product of a community effort to produce Perl code which
|
|
|
|
is useful in biology. Examples include Sequence objects, Alignment objects
|
|
|
|
and database searching objects. These objects not only do what they are
|
|
|
|
advertised to do in the documentation, but they also interact - Alignment
|
|
|
|
objects are made from the Sequence objects, Sequence objects have access to
|
|
|
|
Annotation and SeqFeature objects and databases, Blast objects can be
|
|
|
|
converted to Alignment objects, and so on. This means that the objects
|
|
|
|
provide a coordinated and extensible framework to do computational biology.")
|
|
|
|
(license (package-license perl)))))
|
|
|
|
|
2015-04-15 15:46:35 +00:00
|
|
|
(define-public python-biopython
|
|
|
|
(package
|
|
|
|
(name "python-biopython")
|
|
|
|
(version "1.65")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://biopython.org/DIST/biopython-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(inputs
|
|
|
|
`(("python-numpy" ,python-numpy)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://biopython.org/")
|
|
|
|
(synopsis "Tools for biological computation in Python")
|
|
|
|
(description
|
|
|
|
"Biopython is a set of tools for biological computation including parsers
|
|
|
|
for bioinformatics files into Python data structures; interfaces to common
|
|
|
|
bioinformatics programs; a standard sequence class and tools for performing
|
|
|
|
common operations on them; code to perform data classification; code for
|
|
|
|
dealing with alignments; code making it easy to split up parallelizable tasks
|
|
|
|
into separate processes; and more.")
|
|
|
|
(license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
|
|
|
|
|
|
|
|
(define-public python2-biopython
|
|
|
|
(package (inherit (package-with-python2 python-biopython))
|
|
|
|
(inputs
|
|
|
|
`(("python2-numpy" ,python2-numpy)))))
|
|
|
|
|
2015-06-16 14:24:24 +00:00
|
|
|
(define-public blast+
|
|
|
|
(package
|
|
|
|
(name "blast+")
|
|
|
|
(version "2.2.31")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
|
|
|
|
version "/ncbi-blast-" version "+-src.tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(begin
|
|
|
|
;; Remove bundled bzip2 and zlib
|
|
|
|
(delete-file-recursively "c++/src/util/compress/bzip2")
|
|
|
|
(delete-file-recursively "c++/src/util/compress/zlib")
|
|
|
|
(substitute* "c++/src/util/compress/Makefile.in"
|
|
|
|
(("bzip2 zlib api") "api"))
|
|
|
|
;; Remove useless msbuild directory
|
|
|
|
(delete-file-recursively
|
|
|
|
"c++/src/build-system/project_tree_builder/msbuild")
|
|
|
|
#t))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(;; There are three(!) tests for this massive library, and all fail with
|
|
|
|
;; "unparsable timing stats".
|
|
|
|
;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
|
|
|
|
;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
|
|
|
|
;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
|
|
|
|
#:tests? #f
|
|
|
|
#:out-of-source? #t
|
|
|
|
#:parallel-build? #f ; not supported
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-before
|
|
|
|
'configure 'set-HOME
|
|
|
|
;; $HOME needs to be set at some point during the configure phase
|
|
|
|
(lambda _ (setenv "HOME" "/tmp") #t))
|
|
|
|
(add-after
|
|
|
|
'unpack 'enter-dir
|
|
|
|
(lambda _ (chdir "c++") #t))
|
|
|
|
(add-after
|
|
|
|
'enter-dir 'fix-build-system
|
|
|
|
(lambda _
|
|
|
|
(define (which* cmd)
|
|
|
|
(cond ((string=? cmd "date")
|
|
|
|
;; make call to "date" deterministic
|
|
|
|
"date -d @0")
|
|
|
|
((which cmd)
|
|
|
|
=> identity)
|
|
|
|
(else
|
|
|
|
(format (current-error-port)
|
|
|
|
"WARNING: Unable to find absolute path for ~s~%"
|
|
|
|
cmd)
|
|
|
|
#f)))
|
|
|
|
|
|
|
|
;; Rewrite hardcoded paths to various tools
|
|
|
|
(substitute* (append '("src/build-system/configure.ac"
|
|
|
|
"src/build-system/configure"
|
|
|
|
"scripts/common/impl/if_diff.sh"
|
|
|
|
"scripts/common/impl/run_with_lock.sh"
|
|
|
|
"src/build-system/Makefile.configurables.real"
|
|
|
|
"src/build-system/Makefile.in.top"
|
|
|
|
"src/build-system/Makefile.meta.gmake=no"
|
|
|
|
"src/build-system/Makefile.meta.in"
|
|
|
|
"src/build-system/Makefile.meta_l"
|
|
|
|
"src/build-system/Makefile.meta_p"
|
|
|
|
"src/build-system/Makefile.meta_r"
|
|
|
|
"src/build-system/Makefile.mk.in"
|
|
|
|
"src/build-system/Makefile.requirements"
|
|
|
|
"src/build-system/Makefile.rules_with_autodep.in")
|
|
|
|
(find-files "scripts/common/check" "\\.sh$"))
|
|
|
|
(("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
|
|
|
|
(or (which* cmd) all)))
|
|
|
|
|
|
|
|
(substitute* (find-files "src/build-system" "^config.*")
|
|
|
|
(("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
|
|
|
|
(("^PATH=.*") ""))
|
|
|
|
|
|
|
|
;; rewrite "/var/tmp" in check script
|
|
|
|
(substitute* "scripts/common/check/check_make_unix.sh"
|
|
|
|
(("/var/tmp") "/tmp"))
|
|
|
|
|
|
|
|
;; do not reset PATH
|
|
|
|
(substitute* (find-files "scripts/common/impl/" "\\.sh$")
|
|
|
|
(("^ *PATH=.*") "")
|
|
|
|
(("action=/bin/") "action=")
|
|
|
|
(("export PATH") ":"))
|
|
|
|
#t))
|
|
|
|
(replace
|
|
|
|
'configure
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(let ((out (assoc-ref outputs "out"))
|
|
|
|
(lib (string-append (assoc-ref outputs "lib") "/lib"))
|
|
|
|
(include (string-append (assoc-ref outputs "include")
|
|
|
|
"/include/ncbi-tools++")))
|
|
|
|
;; The 'configure' script doesn't recognize things like
|
|
|
|
;; '--enable-fast-install'.
|
|
|
|
(zero? (system* "./configure.orig"
|
|
|
|
(string-append "--with-build-root=" (getcwd) "/build")
|
|
|
|
(string-append "--prefix=" out)
|
|
|
|
(string-append "--libdir=" lib)
|
|
|
|
(string-append "--includedir=" include)
|
|
|
|
(string-append "--with-bz2="
|
|
|
|
(assoc-ref inputs "bzip2"))
|
|
|
|
(string-append "--with-z="
|
|
|
|
(assoc-ref inputs "zlib"))
|
|
|
|
;; Each library is built twice by default, once
|
|
|
|
;; with "-static" in its name, and again
|
|
|
|
;; without.
|
|
|
|
"--without-static"
|
|
|
|
"--with-dll"))))))))
|
|
|
|
(outputs '("out" ; 19 MB
|
|
|
|
"lib" ; 203 MB
|
|
|
|
"include")) ; 32 MB
|
|
|
|
(inputs
|
|
|
|
`(("bzip2" ,bzip2)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("cpio" ,cpio)))
|
|
|
|
(home-page "http://blast.ncbi.nlm.nih.gov")
|
|
|
|
(synopsis "Basic local alignment search tool")
|
|
|
|
(description
|
|
|
|
"BLAST is a popular method of performing a DNA or protein sequence
|
|
|
|
similarity search, using heuristics to produce results quickly. It also
|
|
|
|
calculates an “expect value” that estimates how many matches would have
|
|
|
|
occurred at a given score by chance, which can aid a user in judging how much
|
|
|
|
confidence to have in an alignment.")
|
|
|
|
;; Most of the sources are in the public domain, with the following
|
|
|
|
;; exceptions:
|
|
|
|
;; * Expat:
|
|
|
|
;; * ./c++/include/util/bitset/
|
|
|
|
;; * ./c++/src/html/ncbi_menu*.js
|
|
|
|
;; * Boost license:
|
|
|
|
;; * ./c++/include/util/impl/floating_point_comparison.hpp
|
|
|
|
;; * LGPL 2+:
|
|
|
|
;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
|
|
|
|
;; * ASL 2.0:
|
|
|
|
;; * ./c++/src/corelib/teamcity_*
|
|
|
|
(license (list license:public-domain
|
|
|
|
license:expat
|
|
|
|
license:boost1.0
|
|
|
|
license:lgpl2.0+
|
|
|
|
license:asl2.0))))
|
|
|
|
|
2014-12-16 16:52:44 +00:00
|
|
|
(define-public bowtie
|
|
|
|
(package
|
|
|
|
(name "bowtie")
|
|
|
|
(version "2.2.4")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
|
|
|
|
version ".tar.gz"))
|
gnu: Add 'file-name' fields for github source tarballs without a name.
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-27 17:23:27 +00:00
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
2014-12-16 16:52:44 +00:00
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(substitute* "Makefile"
|
|
|
|
(("^CC = .*$") "CC = gcc")
|
|
|
|
(("^CPP = .*$") "CPP = g++")
|
|
|
|
;; replace BUILD_HOST and BUILD_TIME for deterministic build
|
|
|
|
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
|
2015-01-29 09:35:52 +00:00
|
|
|
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
|
|
|
|
(patches (list (search-patch "bowtie-fix-makefile.patch")))))
|
2014-12-16 16:52:44 +00:00
|
|
|
(build-system gnu-build-system)
|
|
|
|
(inputs `(("perl" ,perl)
|
|
|
|
("perl-clone" ,perl-clone)
|
|
|
|
("perl-test-deep" ,perl-test-deep)
|
|
|
|
("perl-test-simple" ,perl-test-simple)
|
|
|
|
("python" ,python-2)))
|
|
|
|
(arguments
|
|
|
|
'(#:make-flags '("allall")
|
|
|
|
#:phases
|
|
|
|
(alist-delete
|
|
|
|
'configure
|
|
|
|
(alist-replace
|
|
|
|
'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
|
|
(for-each (lambda (file)
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(install-file file bin))
|
2014-12-16 16:52:44 +00:00
|
|
|
(find-files "." "bowtie2.*"))))
|
|
|
|
(alist-replace
|
|
|
|
'check
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(system* "perl"
|
|
|
|
"scripts/test/simple_tests.pl"
|
|
|
|
"--bowtie2=./bowtie2"
|
|
|
|
"--bowtie2-build=./bowtie2-build"))
|
|
|
|
%standard-phases)))))
|
|
|
|
(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
|
|
|
|
(synopsis "Fast and sensitive nucleotide sequence read aligner")
|
|
|
|
(description
|
|
|
|
"Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
|
|
|
|
reads to long reference sequences. It is particularly good at aligning reads
|
|
|
|
of about 50 up to 100s or 1,000s of characters, and particularly good at
|
|
|
|
aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
|
|
|
|
genome with an FM Index to keep its memory footprint small: for the human
|
|
|
|
genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
|
|
|
|
gapped, local, and paired-end alignment modes.")
|
2015-01-29 09:35:52 +00:00
|
|
|
(supported-systems '("x86_64-linux"))
|
2014-12-16 16:52:44 +00:00
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-03-12 11:35:14 +00:00
|
|
|
(define-public bwa
|
|
|
|
(package
|
|
|
|
(name "bwa")
|
|
|
|
(version "0.7.12")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
|
|
|
|
version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
'(#:tests? #f ;no "check" target
|
|
|
|
#:phases
|
|
|
|
(alist-replace
|
|
|
|
'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append
|
|
|
|
(assoc-ref outputs "out") "/bin"))
|
|
|
|
(doc (string-append
|
|
|
|
(assoc-ref outputs "out") "/share/doc/bwa"))
|
|
|
|
(man (string-append
|
|
|
|
(assoc-ref outputs "out") "/share/man/man1")))
|
|
|
|
(mkdir-p bin)
|
|
|
|
(mkdir-p doc)
|
|
|
|
(mkdir-p man)
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(install-file "bwa" bin)
|
|
|
|
(install-file "README.md" doc)
|
|
|
|
(install-file "bwa.1" man)))
|
2015-03-12 11:35:14 +00:00
|
|
|
;; no "configure" script
|
|
|
|
(alist-delete 'configure %standard-phases))))
|
|
|
|
(inputs `(("zlib" ,zlib)))
|
|
|
|
(home-page "http://bio-bwa.sourceforge.net/")
|
|
|
|
(synopsis "Burrows-Wheeler sequence aligner")
|
|
|
|
(description
|
|
|
|
"BWA is a software package for mapping low-divergent sequences against a
|
|
|
|
large reference genome, such as the human genome. It consists of three
|
|
|
|
algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
|
|
|
|
designed for Illumina sequence reads up to 100bp, while the rest two for
|
|
|
|
longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
|
|
|
|
features such as long-read support and split alignment, but BWA-MEM, which is
|
|
|
|
the latest, is generally recommended for high-quality queries as it is faster
|
|
|
|
and more accurate. BWA-MEM also has better performance than BWA-backtrack for
|
|
|
|
70-100bp Illumina reads.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-03-18 13:39:42 +00:00
|
|
|
(define-public python2-bx-python
|
|
|
|
(package
|
|
|
|
(name "python2-bx-python")
|
|
|
|
(version "0.7.2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://pypi.python.org/packages/source/b/bx-python/bx-python-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(substitute* "setup.py"
|
|
|
|
;; remove dependency on outdated "distribute" module
|
|
|
|
(("^from distribute_setup import use_setuptools") "")
|
|
|
|
(("^use_setuptools\\(\\)") "")))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;tests fail because test data are not included
|
|
|
|
#:python ,python-2))
|
|
|
|
(inputs
|
|
|
|
`(("python-numpy" ,python2-numpy)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-nose" ,python2-nose)
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://bitbucket.org/james_taylor/bx-python/")
|
|
|
|
(synopsis "Tools for manipulating biological data")
|
|
|
|
(description
|
|
|
|
"bx-python provides tools for manipulating biological data, particularly
|
|
|
|
multiple sequence alignments.")
|
|
|
|
(license license:expat)))
|
|
|
|
|
2015-02-25 15:38:17 +00:00
|
|
|
(define-public clipper
|
|
|
|
(package
|
|
|
|
(name "clipper")
|
|
|
|
(version "0.3.0")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/YeoLab/clipper/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
;; remove unnecessary setup dependency
|
|
|
|
'(substitute* "setup.py"
|
|
|
|
(("setup_requires = .*") "")))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments `(#:python ,python-2)) ; only Python 2 is supported
|
|
|
|
(inputs
|
|
|
|
`(("htseq" ,htseq)
|
|
|
|
("python-pybedtools" ,python2-pybedtools)
|
|
|
|
("python-cython" ,python2-cython)
|
|
|
|
("python-scikit-learn" ,python2-scikit-learn)
|
|
|
|
("python-matplotlib" ,python2-matplotlib)
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-scipy" ,python2-scipy)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-mock" ,python2-mock) ; for tests
|
|
|
|
("python-pytz" ,python2-pytz) ; for tests
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "https://github.com/YeoLab/clipper")
|
|
|
|
(synopsis "CLIP peak enrichment recognition")
|
|
|
|
(description
|
|
|
|
"CLIPper is a tool to define peaks in CLIP-seq datasets.")
|
|
|
|
(license license:gpl2)))
|
|
|
|
|
2015-06-03 10:56:16 +00:00
|
|
|
(define-public couger
|
|
|
|
(package
|
|
|
|
(name "couger")
|
|
|
|
(version "1.8.2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://couger.oit.duke.edu/static/assets/COUGER"
|
|
|
|
version ".zip"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(delete 'configure)
|
|
|
|
(delete 'build)
|
|
|
|
(replace
|
|
|
|
'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
(copy-recursively "src" (string-append out "/src"))
|
|
|
|
(mkdir (string-append out "/bin"))
|
|
|
|
;; Add "src" directory to module lookup path.
|
|
|
|
(substitute* "couger"
|
|
|
|
(("from argparse")
|
|
|
|
(string-append "import sys\nsys.path.append(\""
|
|
|
|
out "\")\nfrom argparse")))
|
|
|
|
(copy-file "couger" (string-append out "/bin/couger")))
|
|
|
|
#t))
|
|
|
|
(add-after
|
|
|
|
'install 'wrap-program
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
;; Make sure 'couger' runs with the correct PYTHONPATH.
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
(path (getenv "PYTHONPATH")))
|
|
|
|
(wrap-program (string-append out "/bin/couger")
|
|
|
|
`("PYTHONPATH" ":" prefix (,path))))
|
|
|
|
#t)))))
|
|
|
|
(inputs
|
|
|
|
`(("python" ,python-2)
|
|
|
|
("python2-pillow" ,python2-pillow)
|
|
|
|
("python2-numpy" ,python2-numpy)
|
|
|
|
("python2-scipy" ,python2-scipy)
|
|
|
|
("python2-matplotlib" ,python2-matplotlib)))
|
|
|
|
(propagated-inputs
|
|
|
|
`(("r" ,r)
|
|
|
|
("libsvm" ,libsvm)
|
|
|
|
("randomjungle" ,randomjungle)))
|
|
|
|
(native-inputs
|
|
|
|
`(("unzip" ,unzip)))
|
|
|
|
(home-page "http://couger.oit.duke.edu")
|
|
|
|
(synopsis "Identify co-factors in sets of genomic regions")
|
|
|
|
(description
|
|
|
|
"COUGER can be applied to any two sets of genomic regions bound by
|
|
|
|
paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
|
|
|
|
putative co-factors that provide specificity to each TF. The framework
|
|
|
|
determines the genomic targets uniquely-bound by each TF, and identifies a
|
|
|
|
small set of co-factors that best explain the in vivo binding differences
|
|
|
|
between the two TFs.
|
|
|
|
|
|
|
|
COUGER uses classification algorithms (support vector machines and random
|
|
|
|
forests) with features that reflect the DNA binding specificities of putative
|
|
|
|
co-factors. The features are generated either from high-throughput TF-DNA
|
|
|
|
binding data (from protein binding microarray experiments), or from large
|
|
|
|
collections of DNA motifs.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-03-27 09:09:10 +00:00
|
|
|
(define-public clustal-omega
|
|
|
|
(package
|
|
|
|
(name "clustal-omega")
|
|
|
|
(version "1.2.1")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://www.clustal.org/omega/clustal-omega-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(inputs
|
|
|
|
`(("argtable" ,argtable)))
|
|
|
|
(home-page "http://www.clustal.org/omega/")
|
|
|
|
(synopsis "Multiple sequence aligner for protein and DNA/RNA")
|
|
|
|
(description
|
|
|
|
"Clustal-Omega is a general purpose multiple sequence alignment (MSA)
|
|
|
|
program for protein and DNA/RNA. It produces high quality MSAs and is capable
|
|
|
|
of handling data-sets of hundreds of thousands of sequences in reasonable
|
|
|
|
time.")
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
2015-02-26 15:34:49 +00:00
|
|
|
(define-public crossmap
|
|
|
|
(package
|
|
|
|
(name "crossmap")
|
|
|
|
(version "0.1.6")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
|
|
|
|
;; patch has been sent upstream already
|
|
|
|
(patches (list
|
|
|
|
(search-patch "crossmap-allow-system-pysam.patch")))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
;; remove bundled copy of pysam
|
|
|
|
(snippet
|
|
|
|
'(delete-file-recursively "lib/pysam"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2
|
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'set-env
|
|
|
|
(lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
|
|
|
|
%standard-phases)))
|
|
|
|
(inputs
|
|
|
|
`(("python-numpy" ,python2-numpy)
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
("python-nose" ,python2-nose)
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://crossmap.sourceforge.net/")
|
|
|
|
(synopsis "Convert genome coordinates between assemblies")
|
|
|
|
(description
|
|
|
|
"CrossMap is a program for conversion of genome coordinates or annotation
|
|
|
|
files between different genome assemblies. It supports most commonly used
|
|
|
|
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
2015-03-20 15:17:55 +00:00
|
|
|
(define-public cutadapt
|
|
|
|
(package
|
|
|
|
(name "cutadapt")
|
|
|
|
(version "1.8")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/marcelm/cutadapt/archive/v"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
;; tests must be run after install
|
|
|
|
`(#:phases (alist-cons-after
|
|
|
|
'install 'check
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(setenv "PYTHONPATH"
|
|
|
|
(string-append
|
|
|
|
(getenv "PYTHONPATH")
|
|
|
|
":" (assoc-ref outputs "out")
|
|
|
|
"/lib/python"
|
|
|
|
(string-take (string-take-right
|
|
|
|
(assoc-ref inputs "python") 5) 3)
|
|
|
|
"/site-packages"))
|
|
|
|
(zero? (system* "nosetests" "-P" "tests")))
|
|
|
|
(alist-delete 'check %standard-phases))))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-cython" ,python-cython)
|
|
|
|
("python-nose" ,python-nose)
|
|
|
|
("python-setuptools" ,python-setuptools)))
|
|
|
|
(home-page "https://code.google.com/p/cutadapt/")
|
|
|
|
(synopsis "Remove adapter sequences from nucleotide sequencing reads")
|
|
|
|
(description
|
|
|
|
"Cutadapt finds and removes adapter sequences, primers, poly-A tails and
|
|
|
|
other types of unwanted sequence from high-throughput sequencing reads.")
|
|
|
|
(license license:expat)))
|
|
|
|
|
2015-08-31 15:22:19 +00:00
|
|
|
(define-public deeptools
|
|
|
|
(package
|
|
|
|
(name "deeptools")
|
|
|
|
(version "1.5.11")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/fidelram/deepTools/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1kaagygcbvjs9sxd9cqmskd02wcfp9imvb735r087w7hwqpvz6fs"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2))
|
|
|
|
(propagated-inputs
|
|
|
|
`(("python-scipy" ,python2-scipy)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-matplotlib" ,python2-matplotlib)
|
|
|
|
("python-bx-python" ,python2-bx-python)
|
|
|
|
("python-pysam" ,python2-pysam)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-mock" ,python2-mock) ;for tests
|
|
|
|
("python-pytz" ,python2-pytz) ;for tests
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "https://github.com/fidelram/deepTools")
|
|
|
|
(synopsis "Tools for normalizing and visualizing deep-sequencing data")
|
|
|
|
(description
|
|
|
|
"DeepTools addresses the challenge of handling the large amounts of data
|
|
|
|
that are now routinely generated from DNA sequencing centers. To do so,
|
|
|
|
deepTools contains useful modules to process the mapped reads data to create
|
|
|
|
coverage files in standard bedGraph and bigWig file formats. By doing so,
|
|
|
|
deepTools allows the creation of normalized coverage files or the comparison
|
|
|
|
between two files (for example, treatment and control). Finally, using such
|
|
|
|
normalized and standardized files, multiple visualizations can be created to
|
|
|
|
identify enrichments with functional annotations of the genome.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-06-17 09:21:22 +00:00
|
|
|
(define-public diamond
|
|
|
|
(package
|
|
|
|
(name "diamond")
|
|
|
|
(version "0.7.9")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/bbuchfink/diamond/archive/v"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
|
|
|
|
(snippet '(begin
|
|
|
|
(delete-file "bin/diamond")
|
|
|
|
#t))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
'(#:tests? #f ;no "check" target
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'enter-source-dir
|
|
|
|
(lambda _
|
|
|
|
(chdir "src")
|
|
|
|
#t))
|
|
|
|
(delete 'configure)
|
|
|
|
(replace 'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out")
|
|
|
|
"/bin")))
|
|
|
|
(mkdir-p bin)
|
|
|
|
(copy-file "../bin/diamond"
|
|
|
|
(string-append bin "/diamond"))
|
|
|
|
#t))))))
|
|
|
|
(native-inputs
|
|
|
|
`(("bc" ,bc)))
|
|
|
|
(inputs
|
|
|
|
`(("boost" ,boost)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "https://github.com/bbuchfink/diamond")
|
|
|
|
(synopsis "Accelerated BLAST compatible local sequence aligner")
|
|
|
|
(description
|
|
|
|
"DIAMOND is a BLAST-compatible local aligner for mapping protein and
|
|
|
|
translated DNA query sequences against a protein reference database (BLASTP
|
|
|
|
and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
|
|
|
|
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
|
|
|
|
data and settings.")
|
|
|
|
(license (license:non-copyleft "file://src/COPYING"
|
|
|
|
"See src/COPYING in the distribution."))))
|
|
|
|
|
2015-05-27 13:14:19 +00:00
|
|
|
(define-public edirect
|
|
|
|
(package
|
|
|
|
(name "edirect")
|
|
|
|
(version "2.50")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
;; Note: older versions are not retained.
|
|
|
|
(uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip")
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"08afhz2ph66h8h381hl1mqyxkdi5nbvzsyj9gfw3jfbdijnpi4qj"))))
|
|
|
|
(build-system perl-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(delete 'configure)
|
|
|
|
(delete 'build)
|
|
|
|
(replace 'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((target (string-append (assoc-ref outputs "out")
|
|
|
|
"/bin")))
|
|
|
|
(mkdir-p target)
|
|
|
|
(copy-file "edirect.pl"
|
|
|
|
(string-append target "/edirect.pl"))
|
|
|
|
#t)))
|
|
|
|
(add-after
|
|
|
|
'install 'wrap-program
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
;; Make sure 'edirect.pl' finds all perl inputs at runtime.
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
(path (getenv "PERL5LIB")))
|
|
|
|
(wrap-program (string-append out "/bin/edirect.pl")
|
|
|
|
`("PERL5LIB" ":" prefix (,path)))))))))
|
|
|
|
(inputs
|
|
|
|
`(("perl-html-parser" ,perl-html-parser)
|
|
|
|
("perl-encode-locale" ,perl-encode-locale)
|
|
|
|
("perl-file-listing" ,perl-file-listing)
|
|
|
|
("perl-html-tagset" ,perl-html-tagset)
|
|
|
|
("perl-html-tree" ,perl-html-tree)
|
|
|
|
("perl-http-cookies" ,perl-http-cookies)
|
|
|
|
("perl-http-date" ,perl-http-date)
|
|
|
|
("perl-http-message" ,perl-http-message)
|
|
|
|
("perl-http-negotiate" ,perl-http-negotiate)
|
|
|
|
("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
|
|
|
|
("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
|
|
|
|
("perl-net-http" ,perl-net-http)
|
|
|
|
("perl-uri" ,perl-uri)
|
|
|
|
("perl-www-robotrules" ,perl-www-robotrules)
|
|
|
|
("perl" ,perl)))
|
|
|
|
(native-inputs
|
|
|
|
`(("unzip" ,unzip)))
|
|
|
|
(home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288")
|
|
|
|
(synopsis "Tools for accessing the NCBI's set of databases")
|
|
|
|
(description
|
|
|
|
"Entrez Direct (EDirect) is a method for accessing the National Center
|
|
|
|
for Biotechnology Information's (NCBI) set of interconnected
|
|
|
|
databases (publication, sequence, structure, gene, variation, expression,
|
|
|
|
etc.) from a terminal. Functions take search terms from command-line
|
|
|
|
arguments. Individual operations are combined to build multi-step queries.
|
|
|
|
Record retrieval and formatting normally complete the process.
|
|
|
|
|
|
|
|
EDirect also provides an argument-driven function that simplifies the
|
|
|
|
extraction of data from document summaries or other results that are returned
|
|
|
|
in structured XML format. This can eliminate the need for writing custom
|
|
|
|
software to answer ad hoc questions.")
|
|
|
|
(license license:public-domain)))
|
|
|
|
|
2015-04-16 13:18:10 +00:00
|
|
|
(define-public express
|
|
|
|
(package
|
|
|
|
(name "express")
|
|
|
|
(version "1.5.1")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append
|
|
|
|
"http://bio.math.berkeley.edu/eXpress/downloads/express-"
|
|
|
|
version "/express-" version "-src.tgz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'use-shared-boost-libs-and-set-bamtools-paths
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
(substitute* "CMakeLists.txt"
|
|
|
|
(("set\\(Boost_USE_STATIC_LIBS ON\\)")
|
|
|
|
"set(Boost_USE_STATIC_LIBS OFF)")
|
|
|
|
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
|
|
|
|
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
|
|
|
|
(substitute* "src/CMakeLists.txt"
|
|
|
|
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
|
|
|
|
(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
|
|
|
|
#t)
|
|
|
|
%standard-phases)))
|
|
|
|
(inputs
|
|
|
|
`(("boost" ,boost)
|
|
|
|
("bamtools" ,bamtools)
|
|
|
|
("protobuf" ,protobuf)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "http://bio.math.berkeley.edu/eXpress")
|
|
|
|
(synopsis "Streaming quantification for high-throughput genomic sequencing")
|
|
|
|
(description
|
|
|
|
"eXpress is a streaming tool for quantifying the abundances of a set of
|
|
|
|
target sequences from sampled subsequences. Example applications include
|
|
|
|
transcript-level RNA-Seq quantification, allele-specific/haplotype expression
|
|
|
|
analysis (from RNA-Seq), transcription factor binding quantification in
|
|
|
|
ChIP-Seq, and analysis of metagenomic data.")
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
2015-06-21 06:31:27 +00:00
|
|
|
(define-public fasttree
|
|
|
|
(package
|
|
|
|
(name "fasttree")
|
|
|
|
(version "2.1.8")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://www.microbesonline.org/fasttree/FastTree-"
|
|
|
|
version ".c"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ; no "check" target
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(delete 'unpack)
|
|
|
|
(delete 'configure)
|
|
|
|
(replace 'build
|
|
|
|
(lambda* (#:key source #:allow-other-keys)
|
|
|
|
(and (zero? (system* "gcc"
|
|
|
|
"-O3"
|
|
|
|
"-finline-functions"
|
|
|
|
"-funroll-loops"
|
|
|
|
"-Wall"
|
|
|
|
"-o"
|
|
|
|
"FastTree"
|
|
|
|
source
|
|
|
|
"-lm"))
|
|
|
|
(zero? (system* "gcc"
|
|
|
|
"-DOPENMP"
|
|
|
|
"-fopenmp"
|
|
|
|
"-O3"
|
|
|
|
"-finline-functions"
|
|
|
|
"-funroll-loops"
|
|
|
|
"-Wall"
|
|
|
|
"-o"
|
|
|
|
"FastTreeMP"
|
|
|
|
source
|
|
|
|
"-lm")))))
|
|
|
|
(replace 'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out")
|
|
|
|
"/bin")))
|
|
|
|
(mkdir-p bin)
|
|
|
|
(copy-file "FastTree"
|
|
|
|
(string-append bin "/FastTree"))
|
|
|
|
(copy-file "FastTreeMP"
|
|
|
|
(string-append bin "/FastTreeMP"))
|
|
|
|
#t))))))
|
|
|
|
(home-page "http://www.microbesonline.org/fasttree")
|
|
|
|
(synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
|
|
|
|
(description
|
|
|
|
"FastTree can handle alignments with up to a million of sequences in a
|
|
|
|
reasonable amount of time and memory. For large alignments, FastTree is
|
|
|
|
100-1,000 times faster than PhyML 3.0 or RAxML 7.")
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
2015-04-14 14:36:30 +00:00
|
|
|
(define-public fastx-toolkit
|
|
|
|
(package
|
|
|
|
(name "fastx-toolkit")
|
|
|
|
(version "0.0.14")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append
|
|
|
|
"https://github.com/agordon/fastx_toolkit/releases/download/"
|
|
|
|
version "/fastx_toolkit-" version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(inputs
|
|
|
|
`(("libgtextutils" ,libgtextutils)))
|
|
|
|
(native-inputs
|
|
|
|
`(("pkg-config" ,pkg-config)))
|
|
|
|
(home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
|
|
|
|
(synopsis "Tools for FASTA/FASTQ file preprocessing")
|
|
|
|
(description
|
|
|
|
"The FASTX-Toolkit is a collection of command line tools for Short-Reads
|
|
|
|
FASTA/FASTQ files preprocessing.
|
|
|
|
|
|
|
|
Next-Generation sequencing machines usually produce FASTA or FASTQ files,
|
|
|
|
containing multiple short-reads sequences. The main processing of such
|
|
|
|
FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
|
|
|
|
is sometimes more productive to preprocess the files before mapping the
|
|
|
|
sequences to the genome---manipulating the sequences to produce better mapping
|
|
|
|
results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
|
|
|
|
(license license:agpl3+)))
|
|
|
|
|
2015-02-06 14:42:02 +00:00
|
|
|
(define-public flexbar
|
|
|
|
(package
|
|
|
|
(name "flexbar")
|
|
|
|
(version "2.5")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "mirror://sourceforge/flexbar/"
|
|
|
|
version "/flexbar_v" version "_src.tgz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
2015-04-27 09:48:00 +00:00
|
|
|
`(#:configure-flags (list
|
2015-02-06 14:42:02 +00:00
|
|
|
(string-append "-DFLEXBAR_BINARY_DIR="
|
|
|
|
(assoc-ref %outputs "out")
|
|
|
|
"/bin/"))
|
|
|
|
#:phases
|
2015-04-27 09:48:00 +00:00
|
|
|
(alist-replace
|
|
|
|
'check
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(setenv "PATH" (string-append
|
|
|
|
(assoc-ref outputs "out") "/bin:"
|
|
|
|
(getenv "PATH")))
|
|
|
|
(chdir "../flexbar_v2.5_src/test")
|
|
|
|
(zero? (system* "bash" "flexbar_validate.sh")))
|
|
|
|
(alist-delete 'install %standard-phases))))
|
2015-02-06 14:42:02 +00:00
|
|
|
(inputs
|
|
|
|
`(("tbb" ,tbb)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("pkg-config" ,pkg-config)
|
|
|
|
("seqan" ,seqan)))
|
|
|
|
(home-page "http://flexbar.sourceforge.net")
|
|
|
|
(synopsis "Barcode and adapter removal tool for sequencing platforms")
|
|
|
|
(description
|
|
|
|
"Flexbar preprocesses high-throughput nucleotide sequencing data
|
|
|
|
efficiently. It demultiplexes barcoded runs and removes adapter sequences.
|
|
|
|
Moreover, trimming and filtering features are provided. Flexbar increases
|
|
|
|
read mapping rates and improves genome and transcriptome assemblies. It
|
|
|
|
supports next-generation sequencing data in fasta/q and csfasta/q format from
|
|
|
|
Illumina, Roche 454, and the SOLiD platform.")
|
|
|
|
(license license:gpl3)))
|
|
|
|
|
2015-04-10 09:05:45 +00:00
|
|
|
(define-public grit
|
|
|
|
(package
|
|
|
|
(name "grit")
|
|
|
|
(version "2.0.2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/nboley/grit/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2
|
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'generate-from-cython-sources
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
;; Delete these C files to force fresh generation from pyx sources.
|
|
|
|
(delete-file "grit/sparsify_support_fns.c")
|
|
|
|
(delete-file "grit/call_peaks_support_fns.c")
|
|
|
|
(substitute* "setup.py"
|
|
|
|
(("Cython.Setup") "Cython.Build")
|
|
|
|
;; Add numpy include path to fix compilation
|
|
|
|
(("pyx\", \\]")
|
|
|
|
(string-append "pyx\", ], include_dirs = ['"
|
|
|
|
(assoc-ref inputs "python-numpy")
|
|
|
|
"/lib/python2.7/site-packages/numpy/core/include/"
|
|
|
|
"']"))) #t)
|
|
|
|
%standard-phases)))
|
|
|
|
(inputs
|
|
|
|
`(("python-scipy" ,python2-scipy)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
("python-networkx" ,python2-networkx)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://grit-bio.org")
|
|
|
|
(synopsis "Tool for integrative analysis of RNA-seq type assays")
|
|
|
|
(description
|
|
|
|
"GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
|
|
|
|
full length transcript models. When none of these data sources are available,
|
|
|
|
GRIT can be run by providing a candidate set of TES or TSS sites. In
|
|
|
|
addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
|
|
|
|
also be run in quantification mode, where it uses a provided GTF file and just
|
|
|
|
estimates transcript expression.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-02-09 11:13:26 +00:00
|
|
|
(define-public hisat
|
|
|
|
(package
|
|
|
|
(name "hisat")
|
|
|
|
(version "0.1.4")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://ccb.jhu.edu/software/hisat/downloads/hisat-"
|
|
|
|
version "-beta-source.zip"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
2015-02-12 10:58:40 +00:00
|
|
|
`(#:tests? #f ;no check target
|
|
|
|
#:make-flags '("allall"
|
|
|
|
;; Disable unsupported `popcnt' instructions on
|
|
|
|
;; architectures other than x86_64
|
|
|
|
,@(if (string-prefix? "x86_64"
|
|
|
|
(or (%current-target-system)
|
|
|
|
(%current-system)))
|
|
|
|
'()
|
|
|
|
'("POPCNT_CAPABILITY=0")))
|
2015-02-09 11:13:26 +00:00
|
|
|
#:phases
|
2015-02-27 13:40:21 +00:00
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'patch-sources
|
|
|
|
(lambda _
|
|
|
|
;; XXX Cannot use snippet because zip files are not supported
|
|
|
|
(substitute* "Makefile"
|
|
|
|
(("^CC = .*$") "CC = gcc")
|
|
|
|
(("^CPP = .*$") "CPP = g++")
|
|
|
|
;; replace BUILD_HOST and BUILD_TIME for deterministic build
|
|
|
|
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
|
|
|
|
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
|
|
|
|
(substitute* '("hisat-build" "hisat-inspect")
|
|
|
|
(("/usr/bin/env") (which "env"))))
|
|
|
|
(alist-replace
|
|
|
|
'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bi/")))
|
|
|
|
(for-each (lambda (file)
|
|
|
|
(install-file file bin))
|
|
|
|
(find-files
|
|
|
|
"."
|
|
|
|
"hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
|
2015-02-27 13:40:21 +00:00
|
|
|
(alist-delete 'configure %standard-phases)))))
|
2015-02-09 11:13:26 +00:00
|
|
|
(native-inputs
|
|
|
|
`(("unzip" ,unzip)))
|
|
|
|
(inputs
|
|
|
|
`(("perl" ,perl)
|
|
|
|
("python" ,python)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
|
|
|
|
(synopsis "Hierarchical indexing for spliced alignment of transcripts")
|
|
|
|
(description
|
|
|
|
"HISAT is a fast and sensitive spliced alignment program for mapping
|
|
|
|
RNA-seq reads. In addition to one global FM index that represents a whole
|
|
|
|
genome, HISAT uses a large set of small FM indexes that collectively cover the
|
|
|
|
whole genome. These small indexes (called local indexes) combined with
|
|
|
|
several alignment strategies enable effective alignment of RNA-seq reads, in
|
|
|
|
particular, reads spanning multiple exons.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-06-24 01:51:05 +00:00
|
|
|
(define-public hmmer
|
|
|
|
(package
|
|
|
|
(name "hmmer")
|
|
|
|
(version "3.1b2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://selab.janelia.org/software/hmmer"
|
|
|
|
(version-prefix version 1) "/"
|
|
|
|
version "/hmmer-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(native-inputs `(("perl", perl)))
|
|
|
|
(home-page "http://hmmer.janelia.org")
|
|
|
|
(synopsis "Biosequence analysis using profile hidden Markov models")
|
|
|
|
(description
|
|
|
|
"HMMER is used for searching sequence databases for homologs of protein
|
|
|
|
sequences, and for making protein sequence alignments. It implements methods
|
|
|
|
using probabilistic models called profile hidden Markov models (profile
|
|
|
|
HMMs).")
|
|
|
|
(license (list license:gpl3+
|
|
|
|
;; The bundled library 'easel' is distributed
|
|
|
|
;; under The Janelia Farm Software License.
|
|
|
|
(license:non-copyleft
|
|
|
|
"file://easel/LICENSE"
|
|
|
|
"See easel/LICENSE in the distribution.")))))
|
|
|
|
|
2015-02-20 15:41:50 +00:00
|
|
|
(define-public htseq
|
|
|
|
(package
|
|
|
|
(name "htseq")
|
|
|
|
(version "0.6.1")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments `(#:python ,python-2)) ; only Python 2 is supported
|
|
|
|
(inputs
|
|
|
|
`(("python-numpy" ,python2-numpy)
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://www-huber.embl.de/users/anders/HTSeq/")
|
|
|
|
(synopsis "Analysing high-throughput sequencing data with Python")
|
|
|
|
(description
|
|
|
|
"HTSeq is a Python package that provides infrastructure to process data
|
|
|
|
from high-throughput sequencing assays.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-03-05 09:24:12 +00:00
|
|
|
(define-public htsjdk
|
|
|
|
(package
|
|
|
|
(name "htsjdk")
|
|
|
|
(version "1.129")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/samtools/htsjdk/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
;; remove build dependency on git
|
|
|
|
(snippet '(substitute* "build.xml"
|
|
|
|
(("failifexecutionfails=\"true\"")
|
|
|
|
"failifexecutionfails=\"false\"")))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:modules ((srfi srfi-1)
|
|
|
|
(guix build gnu-build-system)
|
|
|
|
(guix build utils))
|
|
|
|
#:phases (alist-replace
|
|
|
|
'build
|
|
|
|
(lambda _
|
|
|
|
(setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
|
|
|
|
(zero? (system* "ant" "all"
|
|
|
|
(string-append "-Ddist="
|
|
|
|
(assoc-ref %outputs "out")
|
|
|
|
"/share/java/htsjdk/"))))
|
|
|
|
(fold alist-delete %standard-phases
|
|
|
|
'(configure install check)))))
|
|
|
|
(native-inputs
|
|
|
|
`(("ant" ,ant)
|
|
|
|
("jdk" ,icedtea6 "jdk")))
|
|
|
|
(home-page "http://samtools.github.io/htsjdk/")
|
|
|
|
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
|
|
|
|
(description
|
|
|
|
"HTSJDK is an implementation of a unified Java library for accessing
|
|
|
|
common file formats, such as SAM and VCF, used for high-throughput
|
|
|
|
sequencing (HTS) data. There are also an number of useful utilities for
|
|
|
|
manipulating HTS data.")
|
|
|
|
(license license:expat)))
|
|
|
|
|
2015-06-01 13:06:04 +00:00
|
|
|
(define-public htslib
|
|
|
|
(package
|
|
|
|
(name "htslib")
|
|
|
|
(version "1.2.1")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/samtools/htslib/releases/download/"
|
|
|
|
version "/htslib-" version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after
|
|
|
|
'unpack 'patch-tests
|
|
|
|
(lambda _
|
|
|
|
(substitute* "test/test.pl"
|
|
|
|
(("/bin/bash") (which "bash")))
|
|
|
|
#t)))))
|
|
|
|
(inputs
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("perl" ,perl)))
|
|
|
|
(home-page "http://www.htslib.org")
|
|
|
|
(synopsis "C library for reading/writing high-throughput sequencing data")
|
|
|
|
(description
|
|
|
|
"HTSlib is a C library for reading/writing high-throughput sequencing
|
|
|
|
data. It also provides the bgzip, htsfile, and tabix utilities.")
|
|
|
|
;; Files under cram/ are released under the modified BSD license;
|
|
|
|
;; the rest is released under the Expat license
|
|
|
|
(license (list license:expat license:bsd-3))))
|
|
|
|
|
2015-06-16 09:33:26 +00:00
|
|
|
(define-public idr
|
|
|
|
(package
|
|
|
|
(name "idr")
|
|
|
|
(version "2.0.0")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/nboley/idr/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after
|
|
|
|
'install 'wrap-program
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
(python-version (string-take (string-take-right
|
|
|
|
(assoc-ref inputs "python") 5) 3))
|
|
|
|
(path (string-join
|
|
|
|
(map (lambda (name)
|
|
|
|
(string-append (assoc-ref inputs name)
|
|
|
|
"/lib/python" python-version
|
|
|
|
"/site-packages"))
|
|
|
|
'("python-scipy"
|
|
|
|
"python-numpy"
|
|
|
|
"python-matplotlib"))
|
|
|
|
":")))
|
|
|
|
(wrap-program (string-append out "/bin/idr")
|
|
|
|
`("PYTHONPATH" ":" prefix (,path))))
|
|
|
|
#t)))))
|
|
|
|
(inputs
|
|
|
|
`(("python-scipy" ,python-scipy)
|
|
|
|
("python-numpy" ,python-numpy)
|
|
|
|
("python-matplotlib" ,python-matplotlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-cython" ,python-cython)
|
|
|
|
("python-setuptools" ,python-setuptools)))
|
|
|
|
(home-page "https://github.com/nboley/idr")
|
|
|
|
(synopsis "Tool to measure the irreproducible discovery rate (IDR)")
|
|
|
|
(description
|
|
|
|
"The IDR (Irreproducible Discovery Rate) framework is a unified approach
|
|
|
|
to measure the reproducibility of findings identified from replicate
|
|
|
|
experiments and provide highly stable thresholds based on reproducibility.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-02-26 16:10:39 +00:00
|
|
|
(define-public macs
|
|
|
|
(package
|
|
|
|
(name "macs")
|
|
|
|
(version "2.1.0.20140616")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://pypi.python.org/packages/source/M/MACS2/MACS2-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"11lmiw6avqhwn75sn59g4lfkrr2kk20r3rgfbx9xfqb8rg9mi2n6"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2 ; only compatible with Python 2.7
|
|
|
|
#:tests? #f)) ; no test target
|
|
|
|
(inputs
|
|
|
|
`(("python-numpy" ,python2-numpy)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://github.com/taoliu/MACS/")
|
|
|
|
(synopsis "Model based analysis for ChIP-Seq data")
|
|
|
|
(description
|
|
|
|
"MACS is an implementation of a ChIP-Seq analysis algorithm for
|
|
|
|
identifying transcript factor binding sites named Model-based Analysis of
|
|
|
|
ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
|
|
|
|
the significance of enriched ChIP regions and it improves the spatial
|
|
|
|
resolution of binding sites through combining the information of both
|
|
|
|
sequencing tag position and orientation.")
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
2015-07-18 07:39:05 +00:00
|
|
|
|
|
|
|
(define-public metabat
|
|
|
|
(package
|
|
|
|
(name "metabat")
|
|
|
|
(version "0.26.1")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://bitbucket.org/berkeleylab/metabat/get/"
|
|
|
|
version ".tar.bz2"))
|
|
|
|
(file-name (string-append name "-" version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'fix-includes
|
|
|
|
(lambda _
|
2015-07-19 19:25:54 +00:00
|
|
|
(substitute* "SConstruct"
|
|
|
|
(("/include/bam/bam.h")
|
|
|
|
"/include/samtools/bam.h"))
|
|
|
|
(substitute* "src/BamUtils.h"
|
|
|
|
(("^#include \"bam/bam\\.h\"")
|
|
|
|
"#include \"samtools/bam.h\"")
|
|
|
|
(("^#include \"bam/sam\\.h\"")
|
|
|
|
"#include \"samtools/sam.h\""))
|
|
|
|
(substitute* "src/KseqReader.h"
|
|
|
|
(("^#include \"bam/kseq\\.h\"")
|
|
|
|
"#include \"samtools/kseq.h\""))
|
|
|
|
#t))
|
2015-07-18 07:39:05 +00:00
|
|
|
(add-after 'unpack 'fix-scons
|
|
|
|
(lambda _
|
|
|
|
(substitute* "SConstruct" ; Do not distribute README
|
|
|
|
(("^env\\.Install\\(idir_prefix, 'README\\.md'\\)")
|
|
|
|
""))
|
|
|
|
#t))
|
|
|
|
(delete 'configure)
|
|
|
|
(replace 'build
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(mkdir (assoc-ref outputs "out"))
|
|
|
|
(zero? (system* "scons"
|
|
|
|
(string-append
|
|
|
|
"PREFIX="
|
|
|
|
(assoc-ref outputs "out"))
|
|
|
|
(string-append
|
|
|
|
"HTSLIB_DIR="
|
|
|
|
(assoc-ref inputs "htslib"))
|
|
|
|
(string-append
|
|
|
|
"SAMTOOLS_DIR="
|
|
|
|
(assoc-ref inputs "samtools"))
|
|
|
|
(string-append
|
|
|
|
"BOOST_ROOT="
|
|
|
|
(assoc-ref inputs "boost"))
|
|
|
|
"install"))))
|
|
|
|
;; check and install carried out during build phase
|
|
|
|
(delete 'check)
|
|
|
|
(delete 'install))))
|
|
|
|
(inputs
|
|
|
|
`(("zlib" ,zlib)
|
|
|
|
("perl" ,perl)
|
|
|
|
("samtools" ,samtools)
|
|
|
|
("htslib" ,htslib)
|
|
|
|
("boost" ,boost)))
|
|
|
|
(native-inputs
|
|
|
|
`(("scons" ,scons)))
|
|
|
|
(home-page "https://bitbucket.org/berkeleylab/metabat")
|
|
|
|
(synopsis
|
|
|
|
"Reconstruction of single genomes from complex microbial communities")
|
|
|
|
(description
|
|
|
|
"Grouping large genomic fragments assembled from shotgun metagenomic
|
|
|
|
sequences to deconvolute complex microbial communities, or metagenome binning,
|
|
|
|
enables the study of individual organisms and their interactions. MetaBAT is
|
|
|
|
an automated metagenome binning software, which integrates empirical
|
|
|
|
probabilistic distances of genome abundance and tetranucleotide frequency.")
|
|
|
|
(license (license:non-copyleft "file://license.txt"
|
2015-07-19 19:25:54 +00:00
|
|
|
"See license.txt in the distribution."))))
|
2015-07-18 07:39:05 +00:00
|
|
|
|
2015-03-13 09:31:49 +00:00
|
|
|
(define-public miso
|
|
|
|
(package
|
|
|
|
(name "miso")
|
|
|
|
(version "0.5.3")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
2015-06-17 10:16:40 +00:00
|
|
|
"https://pypi.python.org/packages/source/m/misopy/misopy-"
|
2015-03-13 09:31:49 +00:00
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(substitute* "setup.py"
|
2015-06-17 10:14:39 +00:00
|
|
|
;; Use setuptools, or else the executables are not
|
|
|
|
;; installed.
|
|
|
|
(("distutils.core") "setuptools")
|
|
|
|
;; use "gcc" instead of "cc" for compilation
|
2015-03-13 09:31:49 +00:00
|
|
|
(("^defines")
|
|
|
|
"cc.set_executables(
|
|
|
|
compiler='gcc',
|
|
|
|
compiler_so='gcc',
|
|
|
|
linker_exe='gcc',
|
|
|
|
linker_so='gcc -shared'); defines")))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2 ; only Python 2 is supported
|
|
|
|
#:tests? #f)) ; no "test" target
|
|
|
|
(inputs
|
|
|
|
`(("samtools" ,samtools)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
("python-scipy" ,python2-scipy)
|
|
|
|
("python-matplotlib" ,python2-matplotlib)))
|
|
|
|
(native-inputs
|
2015-06-17 10:14:39 +00:00
|
|
|
`(("python-mock" ,python2-mock) ;for tests
|
|
|
|
("python-pytz" ,python2-pytz) ;for tests
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
2015-03-13 09:31:49 +00:00
|
|
|
(home-page "http://genes.mit.edu/burgelab/miso/index.html")
|
|
|
|
(synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
|
|
|
|
(description
|
|
|
|
"MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
|
|
|
|
the expression level of alternatively spliced genes from RNA-Seq data, and
|
|
|
|
identifies differentially regulated isoforms or exons across samples. By
|
|
|
|
modeling the generative process by which reads are produced from isoforms in
|
|
|
|
RNA-Seq, the MISO model uses Bayesian inference to compute the probability
|
|
|
|
that a read originated from a particular isoform.")
|
|
|
|
(license license:gpl2)))
|
|
|
|
|
2015-06-09 14:10:51 +00:00
|
|
|
(define-public orfm
|
|
|
|
(package
|
|
|
|
(name "orfm")
|
2015-06-12 13:08:21 +00:00
|
|
|
(version "0.4.1")
|
2015-06-09 14:10:51 +00:00
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/wwood/OrfM/releases/download/v"
|
|
|
|
version "/orfm-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2015-06-12 13:08:21 +00:00
|
|
|
"05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"))))
|
2015-06-09 14:10:51 +00:00
|
|
|
(build-system gnu-build-system)
|
|
|
|
(inputs `(("zlib" ,zlib)))
|
|
|
|
(synopsis "Simple and not slow open reading frame (ORF) caller")
|
|
|
|
(description
|
|
|
|
"An ORF caller finds stretches of DNA that when translated are not
|
|
|
|
interrupted by stop codons. OrfM finds and prints these ORFs.")
|
|
|
|
(home-page "https://github.com/wwood/OrfM")
|
|
|
|
(license license:lgpl3+)))
|
|
|
|
|
2015-03-20 11:39:50 +00:00
|
|
|
(define-public python2-pbcore
|
|
|
|
(package
|
|
|
|
(name "python2-pbcore")
|
|
|
|
(version "0.9.3")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/PacificBiosciences/pbcore/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1z46rwjac93jm87cbj2zgjg6qvsgs65140wkbbxsvxps7ai4pm09"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
|
|
|
|
(inputs
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
("python-h5py" ,python2-h5py)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "http://pacificbiosciences.github.io/pbcore/")
|
|
|
|
(synopsis "Library for reading and writing PacBio data files")
|
|
|
|
(description
|
|
|
|
"The pbcore package provides Python APIs for interacting with PacBio data
|
|
|
|
files and writing bioinformatics applications.")
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
2015-06-17 10:22:19 +00:00
|
|
|
(define-public python2-warpedlmm
|
|
|
|
(package
|
|
|
|
(name "python2-warpedlmm")
|
|
|
|
(version "0.21")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
|
|
|
|
version ".zip"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2 ; requires Python 2.7
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after
|
|
|
|
'install 'remove-bin-directory
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
;; The "bin" directory only contains wrappers for running
|
|
|
|
;; the module tests. They are not needed after the
|
|
|
|
;; "check" phase.
|
|
|
|
(delete-file-recursively
|
|
|
|
(string-append (assoc-ref outputs "out") "/bin"))
|
|
|
|
#t)))))
|
|
|
|
(propagated-inputs
|
|
|
|
`(("python-scipy" ,python2-scipy)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-matplotlib" ,python2-matplotlib)
|
|
|
|
("python-fastlmm" ,python2-fastlmm)
|
|
|
|
("python-pandas" ,python2-pandas)
|
|
|
|
("python-pysnptools" ,python2-pysnptools)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-setuptools" ,python2-setuptools)
|
|
|
|
("python-mock" ,python2-mock)
|
|
|
|
("python-nose" ,python2-nose)
|
|
|
|
("unzip" ,unzip)))
|
|
|
|
(home-page "https://github.com/PMBio/warpedLMM")
|
|
|
|
(synopsis "Implementation of warped linear mixed models")
|
|
|
|
(description
|
|
|
|
"WarpedLMM is a Python implementation of the warped linear mixed model,
|
|
|
|
which automatically learns an optimal warping function (or transformation) for
|
|
|
|
the phenotype as it models the data.")
|
|
|
|
(license license:asl2.0)))
|
|
|
|
|
2015-03-20 13:36:38 +00:00
|
|
|
(define-public pbtranscript-tofu
|
|
|
|
(let ((commit "c7bbd5472"))
|
|
|
|
(package
|
|
|
|
(name "pbtranscript-tofu")
|
|
|
|
(version (string-append "0.4.1." commit))
|
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/PacificBiosciences/cDNA_primer.git")
|
|
|
|
(commit commit)))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:python ,python-2
|
|
|
|
;; With standard flags, the install phase attempts to create a zip'd
|
|
|
|
;; egg file, and fails with an error: 'ZIP does not support timestamps
|
|
|
|
;; before 1980'
|
|
|
|
#:configure-flags '("--single-version-externally-managed"
|
|
|
|
"--record=pbtranscript-tofu.txt")
|
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'enter-directory-and-clean-up
|
|
|
|
(lambda _
|
|
|
|
(chdir "pbtranscript-tofu/pbtranscript/")
|
|
|
|
;; Delete clutter
|
|
|
|
(delete-file-recursively "dist/")
|
2015-03-31 10:37:31 +00:00
|
|
|
(delete-file-recursively "build/")
|
2015-03-20 13:36:38 +00:00
|
|
|
(delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
|
|
|
|
(delete-file-recursively "pbtools.pbtranscript.egg-info")
|
|
|
|
(delete-file "Cython-0.20.1.tar.gz")
|
|
|
|
(delete-file "setuptools_cython-0.2.1-py2.7.egg")
|
|
|
|
(delete-file "setuptools_cython-0.2.1.tar.gz")
|
|
|
|
(delete-file "setup.cfg")
|
2015-03-31 10:37:31 +00:00
|
|
|
(for-each delete-file
|
|
|
|
(find-files "." "\\.so$"))
|
2015-03-20 13:36:38 +00:00
|
|
|
;; files should be writable for install phase
|
|
|
|
(for-each (lambda (f) (chmod f #o755))
|
2015-03-31 10:37:31 +00:00
|
|
|
(find-files "." "\\.py$")))
|
2015-03-20 13:36:38 +00:00
|
|
|
%standard-phases)))
|
|
|
|
(inputs
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-bx-python" ,python2-bx-python)
|
2015-03-31 11:46:27 +00:00
|
|
|
("python-networkx" ,python2-networkx)
|
|
|
|
("python-scipy" ,python2-scipy)
|
2015-03-20 13:36:38 +00:00
|
|
|
("python-pbcore" ,python2-pbcore)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-nose" ,python2-nose)
|
|
|
|
("python-setuptools" ,python2-setuptools)))
|
|
|
|
(home-page "https://github.com/PacificBiosciences/cDNA_primer")
|
|
|
|
(synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
|
|
|
|
(description
|
|
|
|
"pbtranscript-tofu contains scripts to analyze transcriptome data
|
|
|
|
generated using the PacBio Iso-Seq protocol.")
|
|
|
|
(license license:bsd-3))))
|
|
|
|
|
2015-06-27 12:28:19 +00:00
|
|
|
(define-public prodigal
|
|
|
|
(package
|
|
|
|
(name "prodigal")
|
|
|
|
(version "2.6.2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"https://github.com/hyattpd/Prodigal/archive/v"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;no check target
|
|
|
|
#:make-flags (list (string-append "INSTALLDIR="
|
|
|
|
(assoc-ref %outputs "out")
|
|
|
|
"/bin"))
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(delete 'configure))))
|
|
|
|
(home-page "http://prodigal.ornl.gov")
|
|
|
|
(synopsis "Protein-coding gene prediction for Archaea and Bacteria")
|
|
|
|
(description
|
|
|
|
"Prodigal runs smoothly on finished genomes, draft genomes, and
|
|
|
|
metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
|
|
|
|
format. It runs quickly, in an unsupervised fashion, handles gaps, handles
|
|
|
|
partial genes, and identifies translation initiation sites.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-05-21 13:43:25 +00:00
|
|
|
(define-public rsem
|
|
|
|
(package
|
|
|
|
(name "rsem")
|
|
|
|
(version "1.2.20")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
|
|
|
|
(patches (list (search-patch "rsem-makefile.patch")))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(begin
|
|
|
|
;; remove bundled copy of boost
|
|
|
|
(delete-file-recursively "boost")
|
|
|
|
#t))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
;; No "configure" script.
|
|
|
|
;; Do not build bundled samtools library.
|
|
|
|
(replace 'configure
|
|
|
|
(lambda _
|
|
|
|
(substitute* "Makefile"
|
|
|
|
(("^all : sam/libbam.a") "all : "))
|
|
|
|
#t))
|
|
|
|
(replace 'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let* ((out (string-append (assoc-ref outputs "out")))
|
|
|
|
(bin (string-append out "/bin/"))
|
|
|
|
(perl (string-append out "/lib/perl5/site_perl")))
|
|
|
|
(mkdir-p bin)
|
|
|
|
(mkdir-p perl)
|
|
|
|
(for-each (lambda (file)
|
|
|
|
(copy-file file
|
|
|
|
(string-append bin (basename file))))
|
|
|
|
(find-files "." "rsem-.*"))
|
|
|
|
(copy-file "rsem_perl_utils.pm"
|
|
|
|
(string-append perl "/rsem_perl_utils.pm")))
|
|
|
|
#t))
|
|
|
|
(add-after
|
|
|
|
'install 'wrap-program
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
(for-each (lambda (prog)
|
|
|
|
(wrap-program (string-append out "/bin/" prog)
|
|
|
|
`("PERL5LIB" ":" prefix
|
|
|
|
(,(string-append out "/lib/perl5/site_perl")))))
|
|
|
|
'("rsem-plot-transcript-wiggles"
|
|
|
|
"rsem-calculate-expression"
|
|
|
|
"rsem-generate-ngvector"
|
|
|
|
"rsem-run-ebseq"
|
|
|
|
"rsem-prepare-reference")))
|
|
|
|
#t)))))
|
|
|
|
(inputs
|
|
|
|
`(("boost" ,boost)
|
|
|
|
("ncurses" ,ncurses)
|
|
|
|
("r" ,r)
|
|
|
|
("perl" ,perl)
|
|
|
|
("samtools" ,samtools-0.1)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "http://deweylab.biostat.wisc.edu/rsem/")
|
|
|
|
(synopsis "Estimate gene expression levels from RNA-Seq data")
|
|
|
|
(description
|
|
|
|
"RSEM is a software package for estimating gene and isoform expression
|
|
|
|
levels from RNA-Seq data. The RSEM package provides a user-friendly
|
|
|
|
interface, supports threads for parallel computation of the EM algorithm,
|
|
|
|
single-end and paired-end read data, quality scores, variable-length reads and
|
|
|
|
RSPD estimation. In addition, it provides posterior mean and 95% credibility
|
|
|
|
interval estimates for expression levels. For visualization, it can generate
|
|
|
|
BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-02-18 14:00:04 +00:00
|
|
|
(define-public rseqc
|
|
|
|
(package
|
|
|
|
(name "rseqc")
|
|
|
|
(version "2.6.1")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "mirror://sourceforge/rseqc/"
|
|
|
|
version "/RSeQC-" version ".tar.gz"))
|
|
|
|
(sha256
|
2015-04-13 13:37:40 +00:00
|
|
|
(base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
|
2015-02-18 14:00:04 +00:00
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(begin
|
|
|
|
;; remove bundled copy of pysam
|
|
|
|
(delete-file-recursively "lib/pysam")
|
|
|
|
(substitute* "setup.py"
|
|
|
|
;; remove dependency on outdated "distribute" module
|
|
|
|
(("^from distribute_setup import use_setuptools") "")
|
|
|
|
(("^use_setuptools\\(\\)") "")
|
|
|
|
;; do not use bundled copy of pysam
|
|
|
|
(("^have_pysam = False") "have_pysam = True"))))))
|
|
|
|
(build-system python-build-system)
|
|
|
|
(arguments `(#:python ,python-2))
|
|
|
|
(inputs
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
("python-numpy" ,python2-numpy)
|
|
|
|
("python-setuptools" ,python2-setuptools)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(native-inputs
|
|
|
|
`(("python-nose" ,python2-nose)))
|
|
|
|
(home-page "http://rseqc.sourceforge.net/")
|
|
|
|
(synopsis "RNA-seq quality control package")
|
|
|
|
(description
|
|
|
|
"RSeQC provides a number of modules that can comprehensively evaluate
|
|
|
|
high throughput sequence data, especially RNA-seq data. Some basic modules
|
|
|
|
inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
|
|
|
|
while RNA-seq specific modules evaluate sequencing saturation, mapped reads
|
|
|
|
distribution, coverage uniformity, strand specificity, etc.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2014-12-11 14:48:22 +00:00
|
|
|
(define-public samtools
|
|
|
|
(package
|
|
|
|
(name "samtools")
|
2015-07-02 13:55:00 +00:00
|
|
|
(version "1.2")
|
2014-12-11 14:48:22 +00:00
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "mirror://sourceforge/samtools/"
|
|
|
|
version "/samtools-" version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2015-07-02 13:55:00 +00:00
|
|
|
"1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))))
|
2014-12-11 14:48:22 +00:00
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
2014-12-15 11:36:10 +00:00
|
|
|
`(;; There are 87 test failures when building on non-64-bit architectures
|
|
|
|
;; due to invalid test data. This has since been fixed upstream (see
|
|
|
|
;; <https://github.com/samtools/samtools/pull/307>), but as there has
|
|
|
|
;; not been a new release we disable the tests for all non-64-bit
|
|
|
|
;; systems.
|
|
|
|
#:tests? ,(string=? (or (%current-system) (%current-target-system))
|
|
|
|
"x86_64-linux")
|
2015-07-02 13:53:47 +00:00
|
|
|
#:modules ((ice-9 ftw)
|
|
|
|
(ice-9 regex)
|
|
|
|
(guix build gnu-build-system)
|
|
|
|
(guix build utils))
|
2015-04-23 13:23:26 +00:00
|
|
|
#:make-flags (list "LIBCURSES=-lncurses"
|
|
|
|
(string-append "prefix=" (assoc-ref %outputs "out")))
|
2014-12-11 14:48:22 +00:00
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack
|
2015-04-23 13:23:26 +00:00
|
|
|
'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 "};")))))
|
2015-04-23 14:42:50 +00:00
|
|
|
(alist-cons-after
|
|
|
|
'install 'install-library
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(install-file "libbam.a" lib)))
|
2015-07-02 13:53:47 +00:00
|
|
|
(alist-cons-after
|
|
|
|
'install 'install-headers
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((include (string-append (assoc-ref outputs "out")
|
|
|
|
"/include/samtools/")))
|
|
|
|
(for-each (lambda (file)
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(install-file file include))
|
2015-07-02 13:53:47 +00:00
|
|
|
(scandir "." (lambda (name) (string-match "\\.h$" name))))
|
|
|
|
#t))
|
|
|
|
(alist-delete 'configure %standard-phases))))))
|
2014-12-11 14:48:22 +00:00
|
|
|
(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)))
|
2015-02-06 11:38:40 +00:00
|
|
|
|
2015-04-28 09:28:16 +00:00
|
|
|
(define-public samtools-0.1
|
|
|
|
;; This is the most recent version of the 0.1 line of samtools. The input
|
|
|
|
;; and output formats differ greatly from that used and produced by samtools
|
|
|
|
;; 1.x and is still used in many bioinformatics pipelines.
|
|
|
|
(package (inherit samtools)
|
|
|
|
(version "0.1.19")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "mirror://sourceforge/samtools/"
|
|
|
|
version "/samtools-" version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
|
|
|
|
(arguments
|
|
|
|
(substitute-keyword-arguments (package-arguments samtools)
|
|
|
|
((#:tests? tests) #f) ;no "check" target
|
|
|
|
((#:phases phases)
|
|
|
|
`(modify-phases ,phases
|
|
|
|
(replace 'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append
|
|
|
|
(assoc-ref outputs "out") "/bin")))
|
|
|
|
(mkdir-p bin)
|
|
|
|
(copy-file "samtools"
|
|
|
|
(string-append bin "/samtools")))))
|
|
|
|
(delete 'patch-tests)))))))
|
|
|
|
|
2015-04-14 12:23:19 +00:00
|
|
|
(define-public ngs-sdk
|
|
|
|
(package
|
|
|
|
(name "ngs-sdk")
|
2015-06-01 10:09:44 +00:00
|
|
|
(version "1.1.1")
|
2015-04-14 12:23:19 +00:00
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "https://github.com/ncbi/ngs/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2015-06-01 10:09:44 +00:00
|
|
|
"1x58gpm574n0xmk2a98gmikbgycq78ia0bvnb42k5ck34fmd5v8y"))))
|
2015-04-14 12:23:19 +00:00
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:parallel-build? #f ; not supported
|
|
|
|
#:tests? #f ; no "check" target
|
|
|
|
#:phases
|
|
|
|
(alist-replace
|
|
|
|
'configure
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
;; The 'configure' script doesn't recognize things like
|
|
|
|
;; '--enable-fast-install'.
|
|
|
|
(zero? (system* "./configure"
|
|
|
|
(string-append "--build-prefix=" (getcwd) "/build")
|
|
|
|
(string-append "--prefix=" out)))))
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'enter-dir
|
|
|
|
(lambda _ (chdir "ngs-sdk") #t)
|
|
|
|
%standard-phases))))
|
|
|
|
(native-inputs `(("perl" ,perl)))
|
|
|
|
(home-page "https://github.com/ncbi/ngs")
|
|
|
|
(synopsis "API for accessing Next Generation Sequencing data")
|
|
|
|
(description
|
|
|
|
"NGS is a domain-specific API for accessing reads, alignments and pileups
|
|
|
|
produced from Next Generation Sequencing. The API itself is independent from
|
|
|
|
any particular back-end implementation, and supports use of multiple back-ends
|
|
|
|
simultaneously.")
|
|
|
|
(license license:public-domain)))
|
|
|
|
|
2015-04-14 12:24:01 +00:00
|
|
|
(define-public ngs-java
|
|
|
|
(package (inherit ngs-sdk)
|
|
|
|
(name "ngs-java")
|
|
|
|
(arguments
|
|
|
|
`(,@(substitute-keyword-arguments
|
|
|
|
`(#:modules ((guix build gnu-build-system)
|
|
|
|
(guix build utils)
|
|
|
|
(srfi srfi-1)
|
|
|
|
(srfi srfi-26))
|
|
|
|
,@(package-arguments ngs-sdk))
|
|
|
|
((#:phases phases)
|
|
|
|
`(alist-cons-after
|
|
|
|
'enter-dir 'fix-java-symlink-installation
|
|
|
|
(lambda _
|
|
|
|
;; Only replace the version suffix, not the version number in
|
|
|
|
;; the directory name. Reported here:
|
|
|
|
;; https://github.com/ncbi/ngs/pull/4
|
|
|
|
(substitute* "Makefile.java"
|
|
|
|
(((string-append "\\$\\(subst "
|
|
|
|
"(\\$\\(VERSION[^\\)]*\\)),"
|
|
|
|
"(\\$\\([^\\)]+\\)),"
|
|
|
|
"(\\$\\([^\\)]+\\)|\\$\\@)"
|
|
|
|
"\\)")
|
|
|
|
_ pattern replacement target)
|
|
|
|
(string-append "$(patsubst "
|
|
|
|
"%" pattern ","
|
|
|
|
"%" replacement ","
|
|
|
|
target ")"))))
|
|
|
|
(alist-replace
|
|
|
|
'enter-dir (lambda _ (chdir "ngs-java") #t)
|
|
|
|
,phases))))))
|
|
|
|
(inputs
|
|
|
|
`(("jdk" ,icedtea6 "jdk")
|
|
|
|
("ngs-sdk" ,ngs-sdk)))
|
|
|
|
(synopsis "Java bindings for NGS SDK")))
|
|
|
|
|
2015-04-14 12:42:49 +00:00
|
|
|
(define-public ncbi-vdb
|
|
|
|
(package
|
|
|
|
(name "ncbi-vdb")
|
|
|
|
(version "2.4.5-5")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "https://github.com/ncbi/ncbi-vdb/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:parallel-build? #f ; not supported
|
|
|
|
#:tests? #f ; no "check" target
|
|
|
|
#:phases
|
|
|
|
(alist-replace
|
|
|
|
'configure
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
;; Only replace the version suffix, not the version number in the
|
|
|
|
;; directory name; fixed in commit 4dbba5c6a809 (no release yet).
|
|
|
|
(substitute* "setup/konfigure.perl"
|
|
|
|
(((string-append "\\$\\(subst "
|
|
|
|
"(\\$\\(VERSION[^\\)]*\\)),"
|
|
|
|
"(\\$\\([^\\)]+\\)),"
|
|
|
|
"(\\$\\([^\\)]+\\)|\\$\\@)"
|
|
|
|
"\\)")
|
|
|
|
_ pattern replacement target)
|
|
|
|
(string-append "$(patsubst "
|
|
|
|
"%" pattern ","
|
|
|
|
"%" replacement ","
|
|
|
|
target ")")))
|
|
|
|
|
|
|
|
;; Override include path for libmagic
|
|
|
|
(substitute* "setup/package.prl"
|
|
|
|
(("name => 'magic', Include => '/usr/include'")
|
|
|
|
(string-append "name=> 'magic', Include => '"
|
|
|
|
(assoc-ref inputs "libmagic")
|
|
|
|
"/include" "'")))
|
|
|
|
|
|
|
|
;; Install kdf5 library (needed by sra-tools)
|
|
|
|
(substitute* "build/Makefile.install"
|
|
|
|
(("LIBRARIES_TO_INSTALL =")
|
|
|
|
"LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
|
|
|
|
|
|
|
|
;; The 'configure' script doesn't recognize things like
|
|
|
|
;; '--enable-fast-install'.
|
|
|
|
(zero? (system*
|
|
|
|
"./configure"
|
|
|
|
(string-append "--build-prefix=" (getcwd) "/build")
|
|
|
|
(string-append "--prefix=" (assoc-ref outputs "out"))
|
|
|
|
(string-append "--debug")
|
|
|
|
(string-append "--with-xml2-prefix="
|
|
|
|
(assoc-ref inputs "libxml2"))
|
|
|
|
(string-append "--with-ngs-sdk-prefix="
|
|
|
|
(assoc-ref inputs "ngs-sdk"))
|
|
|
|
(string-append "--with-ngs-java-prefix="
|
|
|
|
(assoc-ref inputs "ngs-java"))
|
|
|
|
(string-append "--with-hdf5-prefix="
|
|
|
|
(assoc-ref inputs "hdf5"))))))
|
|
|
|
(alist-cons-after
|
|
|
|
'install 'install-interfaces
|
2015-06-01 09:31:29 +00:00
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
;; Install interface libraries. On i686 the interface libraries
|
|
|
|
;; are installed to "linux/gcc/i386", so we need to use the Linux
|
|
|
|
;; architecture name ("i386") instead of the target system prefix
|
|
|
|
;; ("i686").
|
2015-04-14 12:42:49 +00:00
|
|
|
(mkdir (string-append (assoc-ref outputs "out") "/ilib"))
|
|
|
|
(copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
|
2015-06-01 09:31:29 +00:00
|
|
|
,(system->linux-architecture
|
|
|
|
(or (%current-target-system)
|
|
|
|
(%current-system)))
|
2015-04-14 12:42:49 +00:00
|
|
|
"/rel/ilib")
|
|
|
|
(string-append (assoc-ref outputs "out")
|
|
|
|
"/ilib"))
|
|
|
|
;; Install interface headers
|
|
|
|
(copy-recursively "interfaces"
|
|
|
|
(string-append (assoc-ref outputs "out")
|
|
|
|
"/include")))
|
|
|
|
%standard-phases))))
|
|
|
|
(inputs
|
|
|
|
`(("libxml2" ,libxml2)
|
|
|
|
("ngs-sdk" ,ngs-sdk)
|
|
|
|
("ngs-java" ,ngs-java)
|
|
|
|
("libmagic" ,file)
|
|
|
|
("hdf5" ,hdf5)))
|
|
|
|
(native-inputs `(("perl" ,perl)))
|
|
|
|
(home-page "https://github.com/ncbi/ncbi-vdb")
|
|
|
|
(synopsis "Database engine for genetic information")
|
|
|
|
(description
|
|
|
|
"The NCBI-VDB library implements a highly compressed columnar data
|
|
|
|
warehousing engine that is most often used to store genetic information.
|
|
|
|
Databases are stored in a portable image within the file system, and can be
|
|
|
|
accessed/downloaded on demand across HTTP.")
|
|
|
|
(license license:public-domain)))
|
|
|
|
|
2015-06-25 10:04:05 +00:00
|
|
|
(define-public plink
|
|
|
|
(package
|
|
|
|
(name "plink")
|
|
|
|
(version "1.07")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
|
|
|
|
version "-src.zip"))
|
|
|
|
(sha256
|
|
|
|
(base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
|
|
|
|
(patches (list (search-patch "plink-1.07-unclobber-i.patch")))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
'(#:tests? #f ;no "check" target
|
|
|
|
#:make-flags (list (string-append "LIB_LAPACK="
|
|
|
|
(assoc-ref %build-inputs "lapack")
|
|
|
|
"/lib/liblapack.so")
|
|
|
|
"WITH_LAPACK=1"
|
|
|
|
"FORCE_DYNAMIC=1"
|
|
|
|
;; disable phoning home
|
|
|
|
"WITH_WEBCHECK=")
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
;; no "configure" script
|
|
|
|
(delete 'configure)
|
|
|
|
(replace 'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out")
|
|
|
|
"/bin/")))
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(install-file "plink" bin)
|
2015-06-25 10:04:05 +00:00
|
|
|
#t))))))
|
|
|
|
(inputs
|
|
|
|
`(("zlib" ,zlib)
|
|
|
|
("lapack" ,lapack)))
|
|
|
|
(native-inputs
|
|
|
|
`(("unzip" ,unzip)))
|
|
|
|
(home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
|
|
|
|
(synopsis "Whole genome association analysis toolset")
|
|
|
|
(description
|
|
|
|
"PLINK is a whole genome association analysis toolset, designed to
|
|
|
|
perform a range of basic, large-scale analyses in a computationally efficient
|
|
|
|
manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
|
|
|
|
so there is no support for steps prior to this (e.g. study design and
|
|
|
|
planning, generating genotype or CNV calls from raw data). Through
|
|
|
|
integration with gPLINK and Haploview, there is some support for the
|
|
|
|
subsequent visualization, annotation and storage of results.")
|
|
|
|
;; Code is released under GPLv2, except for fisher.h, which is under
|
|
|
|
;; LGPLv2.1+
|
|
|
|
(license (list license:gpl2 license:lgpl2.1+))))
|
|
|
|
|
2015-06-23 08:54:00 +00:00
|
|
|
(define-public preseq
|
|
|
|
(package
|
|
|
|
(name "preseq")
|
|
|
|
(version "1.0.2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "http://smithlabresearch.org/downloads/preseq-"
|
|
|
|
version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
|
|
|
|
(patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
|
|
|
|
(search-patch "preseq-1.0.2-link-with-libbam.patch")))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
;; Remove bundled samtools.
|
|
|
|
'(delete-file-recursively "preseq-master/samtools"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after
|
|
|
|
'unpack 'enter-dir
|
|
|
|
(lambda _
|
|
|
|
(chdir "preseq-master")
|
|
|
|
#t))
|
|
|
|
(add-after
|
2015-07-09 10:10:46 +00:00
|
|
|
'enter-dir 'use-samtools-headers
|
2015-06-23 08:54:00 +00:00
|
|
|
(lambda _
|
|
|
|
(substitute* '("smithlab_cpp/SAM.cpp"
|
|
|
|
"smithlab_cpp/SAM.hpp")
|
|
|
|
(("sam.h") "samtools/sam.h"))
|
|
|
|
#t))
|
|
|
|
(delete 'configure))
|
|
|
|
#:make-flags (list (string-append "PREFIX="
|
|
|
|
(assoc-ref %outputs "out"))
|
|
|
|
(string-append "LIBBAM="
|
|
|
|
(assoc-ref %build-inputs "samtools")
|
|
|
|
"/lib/libbam.a"))))
|
|
|
|
(inputs
|
|
|
|
`(("gsl" ,gsl)
|
|
|
|
("samtools" ,samtools-0.1)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "http://smithlabresearch.org/software/preseq/")
|
|
|
|
(synopsis "Program for analyzing library complexity")
|
|
|
|
(description
|
|
|
|
"The preseq package is aimed at predicting and estimating the complexity
|
|
|
|
of a genomic sequencing library, equivalent to predicting and estimating the
|
|
|
|
number of redundant reads from a given sequencing depth and how many will be
|
|
|
|
expected from additional sequencing using an initial sequencing experiment.
|
|
|
|
The estimates can then be used to examine the utility of further sequencing,
|
|
|
|
optimize the sequencing depth, or to screen multiple libraries to avoid low
|
|
|
|
complexity samples.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-04-14 12:43:32 +00:00
|
|
|
(define-public sra-tools
|
|
|
|
(package
|
|
|
|
(name "sra-tools")
|
|
|
|
(version "2.4.5-5")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri
|
|
|
|
(string-append "https://github.com/ncbi/sra-tools/archive/"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:parallel-build? #f ; not supported
|
|
|
|
#:tests? #f ; no "check" target
|
|
|
|
#:phases
|
|
|
|
(alist-replace
|
|
|
|
'configure
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
;; The build system expects a directory containing the sources and
|
|
|
|
;; raw build output of ncbi-vdb, including files that are not
|
|
|
|
;; installed. Since we are building against an installed version of
|
|
|
|
;; ncbi-vdb, the following modifications are needed.
|
|
|
|
(substitute* "setup/konfigure.perl"
|
|
|
|
;; Make the configure script look for the "ilib" directory of
|
|
|
|
;; "ncbi-vdb" without first checking for the existence of a
|
|
|
|
;; matching library in its "lib" directory.
|
|
|
|
(("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
|
|
|
|
"my $f = File::Spec->catdir($ilibdir, $ilib);")
|
|
|
|
;; Look for interface libraries in ncbi-vdb's "ilib" directory.
|
|
|
|
(("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
|
|
|
|
"my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
|
|
|
|
|
|
|
|
;; The 'configure' script doesn't recognize things like
|
|
|
|
;; '--enable-fast-install'.
|
|
|
|
(zero? (system*
|
|
|
|
"./configure"
|
|
|
|
(string-append "--build-prefix=" (getcwd) "/build")
|
|
|
|
(string-append "--prefix=" (assoc-ref outputs "out"))
|
|
|
|
(string-append "--debug")
|
|
|
|
(string-append "--with-fuse-prefix="
|
|
|
|
(assoc-ref inputs "fuse"))
|
|
|
|
(string-append "--with-magic-prefix="
|
|
|
|
(assoc-ref inputs "libmagic"))
|
|
|
|
;; TODO: building with libxml2 fails with linker errors
|
|
|
|
;; (string-append "--with-xml2-prefix="
|
|
|
|
;; (assoc-ref inputs "libxml2"))
|
|
|
|
(string-append "--with-ncbi-vdb-sources="
|
|
|
|
(assoc-ref inputs "ncbi-vdb"))
|
|
|
|
(string-append "--with-ncbi-vdb-build="
|
|
|
|
(assoc-ref inputs "ncbi-vdb"))
|
|
|
|
(string-append "--with-ngs-sdk-prefix="
|
|
|
|
(assoc-ref inputs "ngs-sdk"))
|
|
|
|
(string-append "--with-hdf5-prefix="
|
|
|
|
(assoc-ref inputs "hdf5")))))
|
|
|
|
%standard-phases)))
|
|
|
|
(native-inputs `(("perl" ,perl)))
|
|
|
|
(inputs
|
|
|
|
`(("ngs-sdk" ,ngs-sdk)
|
|
|
|
("ncbi-vdb" ,ncbi-vdb)
|
|
|
|
("libmagic" ,file)
|
|
|
|
("fuse" ,fuse)
|
|
|
|
("hdf5" ,hdf5)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
|
|
|
|
(synopsis "Tools and libraries for reading and writing sequencing data")
|
|
|
|
(description
|
|
|
|
"The SRA Toolkit from NCBI is a collection of tools and libraries for
|
|
|
|
reading of sequencing files from the Sequence Read Archive (SRA) database and
|
|
|
|
writing files into the .sra format.")
|
|
|
|
(license license:public-domain)))
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2015-02-06 11:38:40 +00:00
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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
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(method url-fetch)
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(uri (string-append "http://packages.seqan.de/seqan-library/"
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|
|
|
"seqan-library-" version ".tar.bz2"))
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|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
|
|
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|
;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
|
|
|
|
;; makes sense to split the outputs.
|
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|
(outputs '("out" "doc"))
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(build-system trivial-build-system)
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|
(arguments
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`(#:modules ((guix build utils))
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#:builder
|
|
|
|
(begin
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(use-modules (guix build utils))
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(let ((tar (assoc-ref %build-inputs "tar"))
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(bzip (assoc-ref %build-inputs "bzip2"))
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(out (assoc-ref %outputs "out"))
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|
|
(doc (assoc-ref %outputs "doc")))
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(setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
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|
(system* "tar" "xvf" (assoc-ref %build-inputs "source"))
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(chdir (string-append "seqan-library-" ,version))
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(copy-recursively "include" (string-append out "/include"))
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(copy-recursively "share" (string-append doc "/share"))))))
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|
(native-inputs
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`(("source" ,source)
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|
("tar" ,tar)
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|
|
("bzip2" ,bzip2)))
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|
(home-page "http://www.seqan.de")
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|
(synopsis "Library for nucleotide sequence analysis")
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(description
|
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|
|
"SeqAn is a C++ library of efficient algorithms and data structures for
|
|
|
|
the analysis of sequences with the focus on biological data. It contains
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|
|
algorithms and data structures for string representation and their
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manipulation, online and indexed string search, efficient I/O of
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|
bioinformatics file formats, sequence alignment, and more.")
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(license license:bsd-3)))
|
2015-02-09 14:38:30 +00:00
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|
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|
|
|
|
(define-public star
|
|
|
|
(package
|
|
|
|
(name "star")
|
2015-06-23 16:36:21 +00:00
|
|
|
(version "2.4.2a")
|
2015-02-09 14:38:30 +00:00
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
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|
|
(uri (string-append
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|
|
"https://github.com/alexdobin/STAR/archive/STAR_"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2015-06-23 16:36:21 +00:00
|
|
|
"1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
|
2015-02-09 14:38:30 +00:00
|
|
|
(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/")))
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 20:22:22 +00:00
|
|
|
(install-file "STAR" bin)))
|
2015-02-09 14:38:30 +00:00
|
|
|
(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+)))
|
2015-03-20 15:50:33 +00:00
|
|
|
|
2015-04-16 09:19:45 +00:00
|
|
|
(define-public subread
|
|
|
|
(package
|
|
|
|
(name "subread")
|
|
|
|
(version "1.4.6-p2")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"mirror://sourceforge/subread/subread-"
|
|
|
|
version "-source.tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
#:make-flags '("-f" "Makefile.Linux")
|
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'enter-dir
|
|
|
|
(lambda _ (chdir "src") #t)
|
|
|
|
(alist-replace
|
|
|
|
'install
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
|
|
(mkdir-p bin)
|
|
|
|
(copy-recursively "../bin" bin)))
|
|
|
|
;; no "configure" script
|
|
|
|
(alist-delete 'configure %standard-phases)))))
|
|
|
|
(inputs `(("zlib" ,zlib)))
|
|
|
|
(home-page "http://bioinf.wehi.edu.au/subread-package/")
|
|
|
|
(synopsis "Tool kit for processing next-gen sequencing data")
|
|
|
|
(description
|
|
|
|
"The subread package contains the following tools: subread aligner, a
|
|
|
|
general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
|
|
|
|
and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
|
|
|
|
features; exactSNP: a SNP caller that discovers SNPs by testing signals
|
|
|
|
against local background noises.")
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
2015-03-20 15:50:33 +00:00
|
|
|
(define-public vcftools
|
|
|
|
(package
|
|
|
|
(name "vcftools")
|
|
|
|
(version "0.1.12b")
|
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append
|
|
|
|
"mirror://sourceforge/vcftools/vcftools_"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
`(#:tests? #f ; no "check" target
|
|
|
|
#:make-flags (list
|
2015-05-04 10:17:14 +00:00
|
|
|
"CFLAGS=-O2" ; override "-m64" flag
|
2015-03-20 15:50:33 +00:00
|
|
|
(string-append "PREFIX=" (assoc-ref %outputs "out"))
|
|
|
|
(string-append "MANDIR=" (assoc-ref %outputs "out")
|
|
|
|
"/share/man/man1"))
|
|
|
|
#:phases
|
|
|
|
(alist-cons-after
|
|
|
|
'unpack 'patch-manpage-install
|
|
|
|
(lambda _
|
|
|
|
(substitute* "Makefile"
|
|
|
|
(("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
|
|
|
|
(alist-delete 'configure %standard-phases))))
|
|
|
|
(inputs
|
|
|
|
`(("perl" ,perl)
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
(home-page "http://vcftools.sourceforge.net/")
|
|
|
|
(synopsis "Tools for working with VCF files")
|
|
|
|
(description
|
|
|
|
"VCFtools is a program package designed for working with VCF files, such
|
|
|
|
as those generated by the 1000 Genomes Project. The aim of VCFtools is to
|
|
|
|
provide easily accessible methods for working with complex genetic variation
|
|
|
|
data in the form of VCF files.")
|
|
|
|
;; The license is declared as LGPLv3 in the README and
|
|
|
|
;; at http://vcftools.sourceforge.net/license.html
|
|
|
|
(license license:lgpl3)))
|