2014-12-11 14:48:22 +00:00
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;;; GNU Guix --- Functional package management for GNU
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2016-01-14 13:36:32 +00:00
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;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
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2016-01-10 14:34:11 +00:00
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;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
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2016-02-29 08:37:54 +00:00
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;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
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2015-09-19 22:32:45 +00:00
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;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
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2016-03-10 22:54:31 +00:00
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;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
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2016-03-30 19:45:35 +00:00
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;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
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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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2016-03-14 12:02:48 +00:00
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#:use-module (guix build-system ant)
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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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2015-09-19 22:32:45 +00:00
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#:use-module (guix build-system r)
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2015-09-14 14:32:27 +00:00
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#:use-module (guix build-system ruby)
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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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2015-09-30 08:35:32 +00:00
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#:use-module (gnu packages autotools)
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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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2016-03-10 22:54:31 +00:00
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#:use-module (gnu packages bison)
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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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2016-02-24 16:17:53 +00:00
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#:use-module (gnu packages curl)
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gnu: Update module imports for asciidoc and doxygen.
This is a followup to commit 0573a923def01e54bf104e0015ade44ab42f694f.
* gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm,
gnu/packages/fcitx.scm, gnu/packages/fish.scm,
gnu/packages/freedesktop.scm, gnu/packages/game-development.scm,
gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm,
gnu/packages/kodi.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/messaging.scm,
gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm,
gnu/packages/serialization.scm, gnu/packages/version-control.scm,
gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or
(gnu packages doxygen) to (gnu packages documentation).
2016-05-13 00:18:15 +00:00
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#:use-module (gnu packages documentation)
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2016-02-29 14:13:52 +00:00
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#:use-module (gnu packages datastructures)
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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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2015-12-15 10:34:52 +00:00
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#:use-module (gnu packages gawk)
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2016-01-08 13:18:46 +00:00
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#:use-module (gnu packages gcc)
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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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2015-11-06 14:22:26 +00:00
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#:use-module (gnu packages mpi)
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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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2016-01-06 21:44:58 +00:00
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#:use-module (gnu packages pcre)
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2014-12-11 14:48:22 +00:00
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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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2015-09-14 14:32:27 +00:00
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#:use-module (gnu packages ruby)
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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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2015-12-18 16:40:02 +00:00
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#:use-module (gnu packages time)
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2015-09-30 08:35:32 +00:00
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#:use-module (gnu packages tls)
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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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2016-01-10 14:34:11 +00:00
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(version "2.25.0")
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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"))
|
2014-12-11 16:37:16 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-01-10 14:34:11 +00:00
|
|
|
|
"1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m"))))
|
2014-12-11 16:37:16 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs `(("python" ,python-2)))
|
|
|
|
|
(inputs `(("samtools" ,samtools)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:test-target "test"
|
|
|
|
|
#:phases
|
2016-01-10 14:28:25 +00:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(install-file file bin))
|
|
|
|
|
(find-files "bin" ".*")))
|
|
|
|
|
#t)))))
|
2014-12-11 16:37:16 +00:00
|
|
|
|
(home-page "https://github.com/arq5x/bedtools2")
|
|
|
|
|
(synopsis "Tools for genome analysis and arithmetic")
|
|
|
|
|
(description
|
|
|
|
|
"Collectively, the bedtools utilities are a swiss-army knife of tools for
|
|
|
|
|
a wide-range of genomics analysis tasks. The most widely-used tools enable
|
|
|
|
|
genome arithmetic: that is, set theory on the genome. For example, bedtools
|
|
|
|
|
allows one to intersect, merge, count, complement, and shuffle genomic
|
|
|
|
|
intervals from multiple files in widely-used genomic file formats such as BAM,
|
|
|
|
|
BED, GFF/GTF, VCF.")
|
|
|
|
|
(license license:gpl2)))
|
|
|
|
|
|
2016-03-10 22:54:31 +00:00
|
|
|
|
(define-public bioawk
|
|
|
|
|
(package
|
|
|
|
|
(name "bioawk")
|
|
|
|
|
(version "1.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/lh3/bioawk/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("bison" ,bison)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; There are no tests to run.
|
|
|
|
|
;; Bison must generate files, before other targets can build.
|
|
|
|
|
#:parallel-build? #f
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure) ; There is no configure phase.
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin"))
|
|
|
|
|
(man (string-append out "/share/man/man1")))
|
|
|
|
|
(mkdir-p man)
|
|
|
|
|
(copy-file "awk.1" (string-append man "/bioawk.1"))
|
|
|
|
|
(install-file "bioawk" bin)))))))
|
|
|
|
|
(home-page "https://github.com/lh3/bioawk")
|
|
|
|
|
(synopsis "AWK with bioinformatics extensions")
|
|
|
|
|
(description "Bioawk is an extension to Brian Kernighan's awk, adding the
|
|
|
|
|
support of several common biological data formats, including optionally gzip'ed
|
|
|
|
|
BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
|
|
|
|
|
also adds a few built-in functions and a command line option to use TAB as the
|
|
|
|
|
input/output delimiter. When the new functionality is not used, bioawk is
|
|
|
|
|
intended to behave exactly the same as the original BWK awk.")
|
|
|
|
|
(license license:x11)))
|
|
|
|
|
|
2015-02-20 16:43:08 +00:00
|
|
|
|
(define-public python2-pybedtools
|
|
|
|
|
(package
|
|
|
|
|
(name "python2-pybedtools")
|
|
|
|
|
(version "0.6.9")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(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")
|
2015-11-11 11:27:02 +00:00
|
|
|
|
(version "1.66")
|
2015-04-15 15:46:35 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2015-11-11 11:27:02 +00:00
|
|
|
|
;; use PyPi rather than biopython.org to ease updating
|
|
|
|
|
(uri (pypi-uri "biopython" version))
|
2015-04-15 15:46:35 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2015-11-11 11:27:02 +00:00
|
|
|
|
"1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))
|
2015-04-15 15:46:35 +00:00
|
|
|
|
(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))))
|
|
|
|
|
|
2015-11-06 14:22:26 +00:00
|
|
|
|
(define-public bless
|
|
|
|
|
(package
|
|
|
|
|
(name "bless")
|
|
|
|
|
(version "1p02")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/bless-ec/bless.v"
|
|
|
|
|
version ".tgz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2015-11-06 21:29:02 +00:00
|
|
|
|
"0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
|
|
|
|
|
(modules '((guix build utils)))
|
2015-11-06 14:22:26 +00:00
|
|
|
|
(snippet
|
|
|
|
|
`(begin
|
|
|
|
|
;; Remove bundled boost, pigz, zlib, and .git directory
|
2016-03-14 13:16:55 +00:00
|
|
|
|
;; FIXME: also remove bundled sources for murmurhash3 and
|
|
|
|
|
;; kmc once packaged.
|
2015-11-06 14:22:26 +00:00
|
|
|
|
(delete-file-recursively "boost")
|
|
|
|
|
(delete-file-recursively "pigz")
|
2016-03-14 13:16:55 +00:00
|
|
|
|
(delete-file-recursively "google-sparsehash")
|
2015-11-06 14:22:26 +00:00
|
|
|
|
(delete-file-recursively "zlib")
|
|
|
|
|
(delete-file-recursively ".git")
|
|
|
|
|
#t))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:tests? #f ;no "check" target
|
|
|
|
|
#:make-flags
|
|
|
|
|
(list (string-append "ZLIB="
|
|
|
|
|
(assoc-ref %build-inputs "zlib")
|
|
|
|
|
"/lib/libz.a")
|
|
|
|
|
(string-append "LDFLAGS="
|
|
|
|
|
(string-join '("-lboost_filesystem"
|
|
|
|
|
"-lboost_system"
|
|
|
|
|
"-lboost_iostreams"
|
|
|
|
|
"-lz"
|
|
|
|
|
"-fopenmp"
|
|
|
|
|
"-std=c++11"))))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'do-not-build-bundled-pigz
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(substitute* "Makefile"
|
|
|
|
|
(("cd pigz/pigz-2.3.3; make") ""))
|
|
|
|
|
#t))
|
|
|
|
|
(add-after 'unpack 'patch-paths-to-executables
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(substitute* "parse_args.cpp"
|
|
|
|
|
(("kmc_binary = .*")
|
|
|
|
|
(string-append "kmc_binary = \""
|
|
|
|
|
(assoc-ref outputs "out")
|
|
|
|
|
"/bin/kmc\";"))
|
|
|
|
|
(("pigz_binary = .*")
|
|
|
|
|
(string-append "pigz_binary = \""
|
|
|
|
|
(assoc-ref inputs "pigz")
|
|
|
|
|
"/bin/pigz\";")))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(install-file file bin))
|
|
|
|
|
'("bless" "kmc/bin/kmc"))
|
|
|
|
|
#t)))
|
|
|
|
|
(delete 'configure))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("perl" ,perl)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("openmpi" ,openmpi)
|
|
|
|
|
("boost" ,boost)
|
2016-03-14 13:16:55 +00:00
|
|
|
|
("sparsehash" ,sparsehash)
|
2015-11-06 14:22:26 +00:00
|
|
|
|
("pigz" ,pigz)
|
|
|
|
|
("zlib" ,zlib)))
|
2015-11-20 10:30:57 +00:00
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-11-06 21:29:02 +00:00
|
|
|
|
(home-page "http://sourceforge.net/p/bless-ec/wiki/Home/")
|
2015-11-06 14:22:26 +00:00
|
|
|
|
(synopsis "Bloom-filter-based error correction tool for NGS reads")
|
|
|
|
|
(description
|
|
|
|
|
"@dfn{Bloom-filter-based error correction solution for high-throughput
|
|
|
|
|
sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
|
|
|
|
|
correction tool for genomic reads produced by @dfn{Next-generation
|
|
|
|
|
sequencing} (NGS). BLESS produces accurate correction results with much less
|
|
|
|
|
memory compared with previous solutions and is also able to tolerate a higher
|
|
|
|
|
false-positive rate. BLESS can extend reads like DNA assemblers to correct
|
|
|
|
|
errors at the end of reads.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2014-12-16 16:52:44 +00:00
|
|
|
|
(define-public bowtie
|
|
|
|
|
(package
|
|
|
|
|
(name "bowtie")
|
2016-01-14 13:36:32 +00:00
|
|
|
|
(version "2.2.6")
|
2014-12-16 16:52:44 +00:00
|
|
|
|
(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
|
2016-01-14 13:36:32 +00:00
|
|
|
|
"1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86"))
|
2014-12-16 16:52:44 +00:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(substitute* "Makefile"
|
|
|
|
|
;; replace BUILD_HOST and BUILD_TIME for deterministic build
|
|
|
|
|
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
|
2016-01-14 13:36:32 +00:00
|
|
|
|
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
|
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)
|
2016-01-14 13:36:32 +00:00
|
|
|
|
("python" ,python-2)
|
|
|
|
|
("tbb" ,tbb)))
|
2014-12-16 16:52:44 +00:00
|
|
|
|
(arguments
|
2016-01-14 13:36:32 +00:00
|
|
|
|
'(#:make-flags
|
|
|
|
|
(list "allall"
|
|
|
|
|
"WITH_TBB=1"
|
|
|
|
|
(string-append "prefix=" (assoc-ref %outputs "out")))
|
2014-12-16 16:52:44 +00:00
|
|
|
|
#:phases
|
|
|
|
|
(alist-delete
|
|
|
|
|
'configure
|
|
|
|
|
(alist-replace
|
2016-01-14 13:36:32 +00:00
|
|
|
|
'check
|
2014-12-16 16:52:44 +00:00
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
2016-01-14 13:36:32 +00:00
|
|
|
|
(system* "perl"
|
|
|
|
|
"scripts/test/simple_tests.pl"
|
|
|
|
|
"--bowtie2=./bowtie2"
|
|
|
|
|
"--bowtie2-build=./bowtie2-build"))
|
|
|
|
|
%standard-phases))))
|
2014-12-16 16:52:44 +00:00
|
|
|
|
(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+)))
|
|
|
|
|
|
2016-01-19 13:29:19 +00:00
|
|
|
|
(define-public tophat
|
|
|
|
|
(package
|
|
|
|
|
(name "tophat")
|
|
|
|
|
(version "2.1.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://ccb.jhu.edu/software/tophat/downloads/tophat-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
|
2016-04-08 12:18:13 +00:00
|
|
|
|
(patches (search-patches "tophat-build-with-later-seqan.patch"))
|
2016-01-19 13:29:19 +00:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; Remove bundled SeqAn and samtools
|
|
|
|
|
(delete-file-recursively "src/SeqAn-1.3")
|
|
|
|
|
(delete-file-recursively "src/samtools-0.1.18")
|
|
|
|
|
#t))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:parallel-build? #f ; not supported
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'use-system-samtools
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(substitute* "src/Makefile.in"
|
|
|
|
|
(("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
|
|
|
|
|
(("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
|
|
|
|
|
(("SAMPROG = samtools_0\\.1\\.18") "")
|
|
|
|
|
(("\\$\\(samtools_0_1_18_SOURCES\\)") "")
|
|
|
|
|
(("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
|
|
|
|
|
(substitute* '("src/common.cpp"
|
|
|
|
|
"src/tophat.py")
|
|
|
|
|
(("samtools_0.1.18") (which "samtools")))
|
|
|
|
|
(substitute* '("src/common.h"
|
|
|
|
|
"src/bam2fastx.cpp")
|
|
|
|
|
(("#include \"bam.h\"") "#include <samtools/bam.h>")
|
|
|
|
|
(("#include \"sam.h\"") "#include <samtools/sam.h>"))
|
|
|
|
|
(substitute* '("src/bwt_map.h"
|
|
|
|
|
"src/map2gtf.h"
|
|
|
|
|
"src/align_status.h")
|
|
|
|
|
(("#include <bam.h>") "#include <samtools/bam.h>")
|
|
|
|
|
(("#include <sam.h>") "#include <samtools/sam.h>"))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("boost" ,boost)
|
|
|
|
|
("bowtie" ,bowtie)
|
|
|
|
|
("samtools" ,samtools-0.1)
|
|
|
|
|
("ncurses" ,ncurses)
|
|
|
|
|
("python" ,python-2)
|
|
|
|
|
("perl" ,perl)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("seqan" ,seqan)))
|
|
|
|
|
(home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
|
|
|
|
|
(synopsis "Spliced read mapper for RNA-Seq data")
|
|
|
|
|
(description
|
|
|
|
|
"TopHat is a fast splice junction mapper for nucleotide sequence
|
|
|
|
|
reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
|
|
|
|
|
mammalian-sized genomes using the ultra high-throughput short read
|
|
|
|
|
aligner Bowtie, and then analyzes the mapping results to identify
|
|
|
|
|
splice junctions between exons.")
|
|
|
|
|
;; TopHat is released under the Boost Software License, Version 1.0
|
|
|
|
|
;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
|
|
|
|
|
(license license:boost1.0)))
|
|
|
|
|
|
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)))
|
2015-10-12 13:27:17 +00:00
|
|
|
|
;; Non-portable SSE instructions are used so building fails on platforms
|
|
|
|
|
;; other than x86_64.
|
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-03-12 11:35:14 +00:00
|
|
|
|
(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+)))
|
|
|
|
|
|
2016-02-29 14:13:52 +00:00
|
|
|
|
(define-public bwa-pssm
|
|
|
|
|
(package (inherit bwa)
|
|
|
|
|
(name "bwa-pssm")
|
|
|
|
|
(version "0.5.11")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
|
|
|
|
|
"archive/" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("gdsl" ,gdsl)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("perl" ,perl)))
|
|
|
|
|
(home-page "http://bwa-pssm.binf.ku.dk/")
|
|
|
|
|
(synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
|
|
|
|
|
(description
|
|
|
|
|
"BWA-PSSM is a probabilistic short genomic sequence read aligner based on
|
|
|
|
|
the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
|
|
|
|
|
existing aligners it is fast and sensitive. Unlike most other aligners,
|
|
|
|
|
however, it is also adaptible in the sense that one can direct the alignment
|
|
|
|
|
based on known biases within the data set. It is coded as a modification of
|
|
|
|
|
the original BWA alignment program and shares the genome index structure as
|
|
|
|
|
well as many of the command line options.")
|
|
|
|
|
(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)))
|
|
|
|
|
|
2016-02-25 13:01:14 +00:00
|
|
|
|
(define-public python-pysam
|
|
|
|
|
(package
|
|
|
|
|
(name "python-pysam")
|
2016-02-29 13:36:25 +00:00
|
|
|
|
(version "0.8.4")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (pypi-uri "pysam" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh"))))
|
2016-02-25 13:01:14 +00:00
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; tests are excluded in the manifest
|
|
|
|
|
#:phases
|
|
|
|
|
(alist-cons-before
|
|
|
|
|
'build 'set-flags
|
|
|
|
|
(lambda _
|
|
|
|
|
(setenv "LDFLAGS" "-lncurses")
|
|
|
|
|
(setenv "CFLAGS" "-D_CURSES_LIB=1"))
|
|
|
|
|
%standard-phases)))
|
|
|
|
|
(inputs
|
2016-03-03 12:13:53 +00:00
|
|
|
|
`(("ncurses" ,ncurses)
|
2016-02-25 13:01:14 +00:00
|
|
|
|
("zlib" ,zlib)))
|
2016-03-03 12:13:53 +00:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python-cython" ,python-cython)
|
|
|
|
|
("python-setuptools" ,python-setuptools)))
|
2016-02-25 13:01:14 +00:00
|
|
|
|
(home-page "https://github.com/pysam-developers/pysam")
|
|
|
|
|
(synopsis "Python bindings to the SAMtools C API")
|
|
|
|
|
(description
|
|
|
|
|
"Pysam is a Python module for reading and manipulating files in the
|
|
|
|
|
SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
|
|
|
|
|
also includes an interface for tabix.")
|
|
|
|
|
(license license:expat)))
|
|
|
|
|
|
|
|
|
|
(define-public python2-pysam
|
|
|
|
|
(package-with-python2 python-pysam))
|
|
|
|
|
|
2016-04-06 14:34:19 +00:00
|
|
|
|
(define-public python-twobitreader
|
|
|
|
|
(package
|
|
|
|
|
(name "python-twobitreader")
|
|
|
|
|
(version "3.1.2")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (pypi-uri "twobitreader" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
|
|
|
|
|
(properties `((python2-variant . ,(delay python2-twobitreader))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python-sphinx" ,python-sphinx)))
|
|
|
|
|
(home-page "https://github.com/benjschiller/twobitreader")
|
|
|
|
|
(synopsis "Python library for reading .2bit files")
|
|
|
|
|
(description
|
|
|
|
|
"twobitreader is a Python library for reading .2bit files as used by the
|
|
|
|
|
UCSC genome browser.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
|
|
|
|
(define-public python2-twobitreader
|
|
|
|
|
(let ((base (package-with-python2 (strip-python2-variant python-twobitreader))))
|
|
|
|
|
(package
|
|
|
|
|
(inherit base)
|
|
|
|
|
(native-inputs `(("python2-setuptools" ,python2-setuptools)
|
|
|
|
|
,@(package-native-inputs base))))))
|
|
|
|
|
|
2016-04-06 14:35:09 +00:00
|
|
|
|
(define-public python-plastid
|
|
|
|
|
(package
|
|
|
|
|
(name "python-plastid")
|
|
|
|
|
(version "0.4.5")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (pypi-uri "plastid" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
|
|
|
|
|
(properties `((python2-variant . ,(delay python2-plastid))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
;; Some test files are not included.
|
|
|
|
|
`(#:tests? #f))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("python-numpy" ,python-numpy)
|
|
|
|
|
("python-scipy" ,python-scipy)
|
|
|
|
|
("python-pandas" ,python-pandas)
|
|
|
|
|
("python-pysam" ,python-pysam)
|
|
|
|
|
("python-matplotlib" ,python-matplotlib)
|
|
|
|
|
("python-biopython" ,python-biopython)
|
|
|
|
|
("python-twobitreader" ,python-twobitreader)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python-cython" ,python-cython)
|
|
|
|
|
("python-nose" ,python-nose)))
|
|
|
|
|
(home-page "https://github.com/joshuagryphon/plastid")
|
|
|
|
|
(synopsis "Python library for genomic analysis")
|
|
|
|
|
(description
|
|
|
|
|
"plastid is a Python library for genomic analysis – in particular,
|
|
|
|
|
high-throughput sequencing data – with an emphasis on simplicity.")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
|
|
|
|
(define-public python2-plastid
|
|
|
|
|
(let ((base (package-with-python2 (strip-python2-variant python-plastid))))
|
|
|
|
|
(package
|
|
|
|
|
(inherit base)
|
2016-04-19 14:11:15 +00:00
|
|
|
|
;; setuptools is required at runtime
|
|
|
|
|
(propagated-inputs `(("python2-setuptools" ,python2-setuptools)
|
|
|
|
|
,@(package-propagated-inputs base))))))
|
2016-04-06 14:35:09 +00:00
|
|
|
|
|
2016-03-11 13:57:29 +00:00
|
|
|
|
(define-public cd-hit
|
|
|
|
|
(package
|
|
|
|
|
(name "cd-hit")
|
|
|
|
|
(version "4.6.5")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/weizhongli/cdhit"
|
|
|
|
|
"/releases/download/V" version
|
|
|
|
|
"/cd-hit-v" version "-2016-0304.tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; there are no tests
|
|
|
|
|
#:make-flags
|
|
|
|
|
;; Executables are copied directly to the PREFIX.
|
|
|
|
|
(list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
;; No "configure" script
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
;; Remove sources of non-determinism
|
|
|
|
|
(add-after 'unpack 'be-timeless
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "cdhit-utility.c++"
|
|
|
|
|
((" \\(built on \" __DATE__ \"\\)") ""))
|
|
|
|
|
(substitute* "cdhit-common.c++"
|
|
|
|
|
(("__DATE__") "\"0\"")
|
|
|
|
|
(("\", %s, \" __TIME__ \"\\\\n\", date") ""))
|
|
|
|
|
#t))
|
|
|
|
|
;; The "install" target does not create the target directory
|
|
|
|
|
(add-before 'install 'create-target-dir
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("perl" ,perl)))
|
|
|
|
|
(home-page "http://weizhongli-lab.org/cd-hit/")
|
|
|
|
|
(synopsis "Cluster and compare protein or nucleotide sequences")
|
|
|
|
|
(description
|
|
|
|
|
"CD-HIT is a program for clustering and comparing protein or nucleotide
|
|
|
|
|
sequences. CD-HIT is designed to be fast and handle extremely large
|
|
|
|
|
databases.")
|
|
|
|
|
;; The manual says: "It can be copied under the GNU General Public License
|
|
|
|
|
;; version 2 (GPLv2)."
|
|
|
|
|
(license license:gpl2)))
|
|
|
|
|
|
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"))
|
2015-10-02 14:54:20 +00:00
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
2015-02-25 15:38:17 +00:00
|
|
|
|
(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)))
|
|
|
|
|
|
2016-03-11 03:47:24 +00:00
|
|
|
|
(define-public codingquarry
|
|
|
|
|
(package
|
|
|
|
|
(name "codingquarry")
|
|
|
|
|
(version "2.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"mirror://sourceforge/codingquarry/CodingQuarry_v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:tests? #f ; no "check" target
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin"))
|
|
|
|
|
(doc (string-append out "/share/doc/codingquarry")))
|
|
|
|
|
(install-file "INSTRUCTIONS.pdf" doc)
|
|
|
|
|
(copy-recursively "QuarryFiles"
|
|
|
|
|
(string-append out "/QuarryFiles"))
|
|
|
|
|
(install-file "CodingQuarry" bin)
|
|
|
|
|
(install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
|
|
|
|
|
(inputs `(("openmpi" ,openmpi)))
|
|
|
|
|
(native-search-paths
|
|
|
|
|
(list (search-path-specification
|
|
|
|
|
(variable "QUARRY_PATH")
|
|
|
|
|
(files '("QuarryFiles")))))
|
|
|
|
|
(native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
|
|
|
|
|
(synopsis "Fungal gene predictor")
|
|
|
|
|
(description "CodingQuarry is a highly accurate, self-training GHMM fungal
|
|
|
|
|
gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
|
|
|
|
|
(home-page "https://sourceforge.net/projects/codingquarry/")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
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")
|
2015-10-27 10:12:32 +00:00
|
|
|
|
(version "0.2.1")
|
2015-02-26 15:34:49 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2015-10-27 10:12:32 +00:00
|
|
|
|
"07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
|
|
|
|
|
;; This patch has been sent upstream already and is available
|
|
|
|
|
;; for download from Sourceforge, but it has not been merged.
|
2016-04-08 12:18:13 +00:00
|
|
|
|
(patches (search-patches "crossmap-allow-system-pysam.patch"))
|
2015-02-26 15:34:49 +00:00
|
|
|
|
(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+)))
|
|
|
|
|
|
2015-09-16 15:42:41 +00:00
|
|
|
|
(define-public cufflinks
|
|
|
|
|
(package
|
|
|
|
|
(name "cufflinks")
|
|
|
|
|
(version "2.2.1")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://cole-trapnell-lab.github.io/"
|
|
|
|
|
"cufflinks/assets/downloads/cufflinks-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:make-flags
|
|
|
|
|
(list
|
|
|
|
|
;; The includes for "eigen" are located in a subdirectory.
|
|
|
|
|
(string-append "EIGEN_CPPFLAGS="
|
|
|
|
|
"-I" (assoc-ref %build-inputs "eigen")
|
|
|
|
|
"/include/eigen3/")
|
|
|
|
|
;; Cufflinks must be linked with various boost libraries.
|
|
|
|
|
(string-append "LDFLAGS="
|
|
|
|
|
(string-join '("-lboost_system"
|
|
|
|
|
"-lboost_serialization"
|
|
|
|
|
"-lboost_thread"))))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'fix-search-for-bam
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* '("ax_bam.m4"
|
|
|
|
|
"configure"
|
|
|
|
|
"src/hits.h")
|
|
|
|
|
(("<bam/sam\\.h>") "<samtools/sam.h>")
|
|
|
|
|
(("<bam/bam\\.h>") "<samtools/bam.h>")
|
|
|
|
|
(("<bam/version\\.hpp>") "<samtools/version.h>"))
|
|
|
|
|
#t)))
|
|
|
|
|
#:configure-flags
|
|
|
|
|
(list (string-append "--with-bam="
|
|
|
|
|
(assoc-ref %build-inputs "samtools")))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("eigen" ,eigen)
|
|
|
|
|
("samtools" ,samtools-0.1)
|
|
|
|
|
("htslib" ,htslib)
|
|
|
|
|
("boost" ,boost)
|
|
|
|
|
("python" ,python-2)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(home-page "http://cole-trapnell-lab.github.io/cufflinks/")
|
|
|
|
|
(synopsis "Transcriptome assembly and RNA-Seq expression analysis")
|
|
|
|
|
(description
|
|
|
|
|
"Cufflinks assembles RNA transcripts, estimates their abundances,
|
|
|
|
|
and tests for differential expression and regulation in RNA-Seq
|
|
|
|
|
samples. It accepts aligned RNA-Seq reads and assembles the
|
|
|
|
|
alignments into a parsimonious set of transcripts. Cufflinks then
|
|
|
|
|
estimates the relative abundances of these transcripts based on how
|
|
|
|
|
many reads support each one, taking into account biases in library
|
|
|
|
|
preparation protocols.")
|
|
|
|
|
(license license:boost1.0)))
|
|
|
|
|
|
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)))
|
|
|
|
|
|
2016-02-24 16:17:53 +00:00
|
|
|
|
(define-public libbigwig
|
|
|
|
|
(package
|
|
|
|
|
(name "libbigwig")
|
|
|
|
|
(version "0.1.4")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/dpryan79/libBigWig/"
|
|
|
|
|
"archive/" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:test-target "test"
|
|
|
|
|
#:make-flags
|
|
|
|
|
(list "CC=gcc"
|
|
|
|
|
(string-append "prefix=" (assoc-ref %outputs "out")))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(add-before 'check 'disable-curl-test
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "Makefile"
|
|
|
|
|
(("./test/testRemote.*") ""))
|
|
|
|
|
#t))
|
|
|
|
|
;; This has been fixed with the upstream commit 4ff6959cd8a0, but
|
|
|
|
|
;; there has not yet been a release containing this change.
|
|
|
|
|
(add-before 'install 'create-target-dirs
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
|
(mkdir-p (string-append out "/lib"))
|
|
|
|
|
(mkdir-p (string-append out "/include"))
|
|
|
|
|
#t))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)
|
|
|
|
|
("curl" ,curl)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("doxygen" ,doxygen)))
|
|
|
|
|
(home-page "https://github.com/dpryan79/libBigWig")
|
|
|
|
|
(synopsis "C library for handling bigWig files")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides a C library for parsing local and remote BigWig
|
|
|
|
|
files.")
|
|
|
|
|
(license license:expat)))
|
|
|
|
|
|
2016-02-29 13:37:38 +00:00
|
|
|
|
(define-public python-pybigwig
|
|
|
|
|
(package
|
|
|
|
|
(name "python-pybigwig")
|
|
|
|
|
(version "0.2.5")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (pypi-uri "pyBigWig" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; Delete bundled libBigWig sources
|
|
|
|
|
(delete-file-recursively "libBigWig")))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'link-with-libBigWig
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(substitute* "setup.py"
|
|
|
|
|
(("libs=\\[") "libs=[\"BigWig\", "))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("libbigwig" ,libbigwig)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("curl" ,curl)))
|
|
|
|
|
(home-page "https://github.com/dpryan79/pyBigWig")
|
|
|
|
|
(synopsis "Access bigWig files in Python using libBigWig")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides Python bindings to the libBigWig library for
|
|
|
|
|
accessing bigWig files.")
|
|
|
|
|
(license license:expat)))
|
|
|
|
|
|
|
|
|
|
(define-public python2-pybigwig
|
|
|
|
|
(let ((pybigwig (package-with-python2 python-pybigwig)))
|
|
|
|
|
(package (inherit pybigwig)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python-setuptools" ,python2-setuptools))))))
|
|
|
|
|
|
2015-08-31 15:22:19 +00:00
|
|
|
|
(define-public deeptools
|
|
|
|
|
(package
|
|
|
|
|
(name "deeptools")
|
2016-02-29 13:40:10 +00:00
|
|
|
|
(version "2.1.1")
|
2015-08-31 15:22:19 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-02-29 13:40:10 +00:00
|
|
|
|
(uri (string-append "https://github.com/fidelram/deepTools/"
|
|
|
|
|
"archive/" version ".tar.gz"))
|
2015-08-31 15:22:19 +00:00
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-02-29 13:40:10 +00:00
|
|
|
|
"1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
|
2015-08-31 15:22:19 +00:00
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:python ,python-2))
|
2016-02-29 13:38:57 +00:00
|
|
|
|
(inputs
|
2015-08-31 15:22:19 +00:00
|
|
|
|
`(("python-scipy" ,python2-scipy)
|
|
|
|
|
("python-numpy" ,python2-numpy)
|
2016-02-29 13:40:10 +00:00
|
|
|
|
("python-numpydoc" ,python2-numpydoc)
|
2015-08-31 15:22:19 +00:00
|
|
|
|
("python-matplotlib" ,python2-matplotlib)
|
|
|
|
|
("python-bx-python" ,python2-bx-python)
|
2016-02-29 13:40:10 +00:00
|
|
|
|
("python-pysam" ,python2-pysam)
|
|
|
|
|
("python-pybigwig" ,python2-pybigwig)))
|
2015-08-31 15:22:19 +00:00
|
|
|
|
(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.")
|
2015-10-14 10:21:43 +00:00
|
|
|
|
;; diamond fails to build on other platforms
|
|
|
|
|
;; https://github.com/bbuchfink/diamond/issues/18
|
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-06-17 09:21:22 +00:00
|
|
|
|
(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")
|
2016-05-04 14:44:55 +00:00
|
|
|
|
(version "4.10")
|
2015-05-27 13:14:19 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-05-04 14:44:55 +00:00
|
|
|
|
(uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
|
|
|
|
|
"versions/2016-05-03/edirect.tar.gz"))
|
2015-05-27 13:14:19 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-04 14:44:55 +00:00
|
|
|
|
"15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
|
2015-05-27 13:14:19 +00:00
|
|
|
|
(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)))
|
2015-11-20 14:17:00 +00:00
|
|
|
|
(home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
|
2015-05-27 13:14:19 +00:00
|
|
|
|
(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)))
|
|
|
|
|
|
2015-10-15 12:53:31 +00:00
|
|
|
|
(define-public express-beta-diversity
|
|
|
|
|
(package
|
|
|
|
|
(name "express-beta-diversity")
|
|
|
|
|
(version "1.0.7")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri
|
|
|
|
|
(string-append
|
|
|
|
|
"https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(add-before 'build 'enter-source (lambda _ (chdir "source") #t))
|
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
|
|
|
|
|
"-u"))))
|
|
|
|
|
(add-after 'check 'exit-source (lambda _ (chdir "..") #t))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out")
|
|
|
|
|
"/bin")))
|
|
|
|
|
(mkdir-p bin)
|
|
|
|
|
(copy-file "scripts/convertToEBD.py"
|
|
|
|
|
(string-append bin "/convertToEBD.py"))
|
|
|
|
|
(copy-file "bin/ExpressBetaDiversity"
|
|
|
|
|
(string-append bin "/ExpressBetaDiversity"))
|
|
|
|
|
#t))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("python" ,python-2)))
|
|
|
|
|
(home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
|
|
|
|
|
(synopsis "Taxon- and phylogenetic-based beta diversity measures")
|
|
|
|
|
(description
|
|
|
|
|
"Express Beta Diversity (EBD) calculates ecological beta diversity
|
|
|
|
|
(dissimilarity) measures between biological communities. EBD implements a
|
|
|
|
|
variety of diversity measures including those that make use of phylogenetic
|
|
|
|
|
similarity of community members.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
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)))
|
|
|
|
|
|
2015-12-27 21:53:27 +00:00
|
|
|
|
(define-public fraggenescan
|
|
|
|
|
(package
|
|
|
|
|
(name "fraggenescan")
|
|
|
|
|
(version "1.20")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri
|
|
|
|
|
(string-append "mirror://sourceforge/fraggenescan/"
|
|
|
|
|
"FragGeneScan" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(add-before 'build 'patch-paths
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (string-append (assoc-ref outputs "out")))
|
|
|
|
|
(share (string-append out "/share/fraggenescan/")))
|
|
|
|
|
(substitute* "run_FragGeneScan.pl"
|
|
|
|
|
(("system\\(\"rm")
|
|
|
|
|
(string-append "system(\"" (which "rm")))
|
|
|
|
|
(("system\\(\"mv")
|
|
|
|
|
(string-append "system(\"" (which "mv")))
|
|
|
|
|
;; This script and other programs expect the training files
|
|
|
|
|
;; to be in the non-standard location bin/train/XXX. Change
|
|
|
|
|
;; this to be share/fraggenescan/train/XXX instead.
|
|
|
|
|
(("^\\$train.file = \\$dir.*")
|
|
|
|
|
(string-append "$train_file = \""
|
|
|
|
|
share
|
|
|
|
|
"train/\".$FGS_train_file;")))
|
|
|
|
|
(substitute* "run_hmm.c"
|
|
|
|
|
(("^ strcat\\(train_dir, \\\"train/\\\"\\);")
|
|
|
|
|
(string-append " strcpy(train_dir, \"" share "/train/\");")))
|
|
|
|
|
(substitute* "post_process.pl"
|
|
|
|
|
(("^my \\$dir = substr.*")
|
|
|
|
|
(string-append "my $dir = \"" share "\";"))))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'build
|
|
|
|
|
(lambda _ (and (zero? (system* "make" "clean"))
|
|
|
|
|
(zero? (system* "make" "fgs")))))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (string-append (assoc-ref outputs "out")))
|
|
|
|
|
(bin (string-append out "/bin/"))
|
|
|
|
|
(share (string-append out "/share/fraggenescan/train")))
|
|
|
|
|
(install-file "run_FragGeneScan.pl" bin)
|
|
|
|
|
(install-file "FragGeneScan" bin)
|
|
|
|
|
(install-file "FGS_gff.py" bin)
|
|
|
|
|
(install-file "post_process.pl" bin)
|
|
|
|
|
(copy-recursively "train" share))))
|
|
|
|
|
(delete 'check)
|
|
|
|
|
(add-after 'install 'post-install-check
|
|
|
|
|
;; In lieu of 'make check', run one of the examples and check the
|
|
|
|
|
;; output files gets created.
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (string-append (assoc-ref outputs "out")))
|
|
|
|
|
(bin (string-append out "/bin/")))
|
|
|
|
|
(and (zero? (system* (string-append bin "run_FragGeneScan.pl")
|
|
|
|
|
"-genome=./example/NC_000913.fna"
|
|
|
|
|
"-out=./test2"
|
|
|
|
|
"-complete=1"
|
|
|
|
|
"-train=complete"))
|
|
|
|
|
(file-exists? "test2.faa")
|
|
|
|
|
(file-exists? "test2.ffn")
|
|
|
|
|
(file-exists? "test2.gff")
|
|
|
|
|
(file-exists? "test2.out"))))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("perl" ,perl)
|
|
|
|
|
("python" ,python-2))) ;not compatible with python 3.
|
|
|
|
|
(home-page "https://sourceforge.net/projects/fraggenescan/")
|
|
|
|
|
(synopsis "Finds potentially fragmented genes in short reads")
|
|
|
|
|
(description
|
|
|
|
|
"FragGeneScan is a program for predicting bacterial and archaeal genes in
|
|
|
|
|
short and error-prone DNA sequencing reads. It can also be applied to predict
|
|
|
|
|
genes in incomplete assemblies or complete genomes.")
|
|
|
|
|
;; GPL3+ according to private correspondense with the authors.
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2016-01-06 21:44:58 +00:00
|
|
|
|
(define-public fxtract
|
|
|
|
|
(let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
|
|
|
|
|
(package
|
|
|
|
|
(name "fxtract")
|
|
|
|
|
(version "2.3")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/ctSkennerton/fxtract/archive/"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append "ctstennerton-util-"
|
|
|
|
|
(string-take util-commit 7)
|
|
|
|
|
"-checkout"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:make-flags (list
|
|
|
|
|
(string-append "PREFIX=" (assoc-ref %outputs "out"))
|
|
|
|
|
"CC=gcc")
|
|
|
|
|
#:test-target "fxtract_test"
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(add-before 'build 'copy-util
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(rmdir "util")
|
|
|
|
|
(copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
|
|
|
|
|
#t))
|
|
|
|
|
;; Do not use make install as this requires additional dependencies.
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out"/bin")))
|
|
|
|
|
(install-file "fxtract" bin)
|
|
|
|
|
#t))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("pcre" ,pcre)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
;; ctskennerton-util is licensed under GPL2.
|
|
|
|
|
`(("ctskennerton-util"
|
|
|
|
|
,(origin
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference
|
|
|
|
|
(url "https://github.com/ctSkennerton/util.git")
|
|
|
|
|
(commit util-commit)))
|
|
|
|
|
(file-name (string-append
|
|
|
|
|
"ctstennerton-util-" util-commit "-checkout"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
|
|
|
|
|
(home-page "https://github.com/ctSkennerton/fxtract")
|
|
|
|
|
(synopsis "Extract sequences from FASTA and FASTQ files")
|
|
|
|
|
(description
|
|
|
|
|
"Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
|
|
|
|
|
or FASTQ) file given a subsequence. It uses a simple substring search for
|
|
|
|
|
basic tasks but can change to using POSIX regular expressions, PCRE, hash
|
|
|
|
|
lookups or multi-pattern searching as required. By default fxtract looks in
|
|
|
|
|
the sequence of each record but can also be told to look in the header,
|
|
|
|
|
comment or quality sections.")
|
|
|
|
|
(license license:expat))))
|
|
|
|
|
|
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)))
|
2015-11-02 13:36:36 +00:00
|
|
|
|
;; Non-portable SSE instructions are used so building fails on platforms
|
|
|
|
|
;; other than x86_64.
|
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-02-09 11:13:26 +00:00
|
|
|
|
(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
|
2016-05-16 11:28:53 +00:00
|
|
|
|
"http://eddylab.org/software/hmmer"
|
2015-06-24 01:51:05 +00:00
|
|
|
|
(version-prefix version 1) "/"
|
|
|
|
|
version "/hmmer-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
|
|
|
|
|
(build-system gnu-build-system)
|
gnu: Fix misplaced commas (unquote).
Fix many occurrences of comma (unquote) being placed immediately after the
previous list item, e.g. ("ncurses", ncurses) in the inputs.
* gnu/packages/base.scm (patch, gnu-make),
gnu/packages/bioinformatics.scm (hmmer),
gnu/packages/bittorrent.scm (aria2),
gnu/packages/compression.scm (pbzip2),
gnu/packages/databases.scm (recutils),
gnu/packages/fonts.scm (font-terminus),
gnu/packages/freedesktop.scm (xdg-utils, elogind),
gnu/packages/games.scm (gnujump),
gnu/packages/gnome.scm (libidl, gnumeric, eog, gedit),
gnu/packages/gnunet.scm (gnunet),
gnu/packages/gnuzilla.scm (mozjs, nspr),
gnu/packages/gtk.scm (gtksourceview, gdk-pixbuf),
gnu/packages/lua.scm (lua),
gnu/packages/openstack.scm (python-swiftclient),
gnu/packages/perl.scm (perl-json-any),
gnu/packages/polkit.scm (polkit-qt),
gnu/packages/python.scm (wrap-python3, python-oauthlib)
(python-mccabe-0.2.1, python-contextlib2, python2-rauth),
gnu/packages/qt.scm (qtkeychain),
gnu/packages/ruby.scm (ruby-nokogiri),
gnu/packages/screen.scm (screen),
gnu/packages/ssh.scm (libssh),
gnu/packages/video.scm (ffmpeg, mplayer),
gnu/packages/vim.scm (vim),
gnu/packages/xdisorg.scm (redshift),
gnu/packages/xfce.scm (xfce4-panel, xfce4-settings),
gnu/packages/xnee.scm (xnee),
gnu/packages/xorg.scm (font-adobe100dpi, font-adobe75dpi),
gnu/packages/zsh.scm (zsh): Fix misplaced commas (unquote).
2016-02-27 13:37:28 +00:00
|
|
|
|
(native-inputs `(("perl" ,perl)))
|
2016-05-16 11:28:53 +00:00
|
|
|
|
(home-page "http://hmmer.org/")
|
2015-06-24 01:51:05 +00:00
|
|
|
|
(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
|
2015-11-20 10:29:37 +00:00
|
|
|
|
;; Numpy needs to be propagated when htseq is used as a Python library.
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("python-numpy" ,python2-numpy)))
|
2016-02-08 15:55:40 +00:00
|
|
|
|
(inputs
|
|
|
|
|
`(("python-pysam" ,python2-pysam)))
|
2015-11-20 10:29:37 +00:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python-setuptools" ,python2-setuptools)))
|
2015-02-20 15:41:50 +00:00
|
|
|
|
(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+)))
|
|
|
|
|
|
2016-04-16 08:51:23 +00:00
|
|
|
|
(define-public java-htsjdk
|
2015-03-05 09:24:12 +00:00
|
|
|
|
(package
|
2016-04-16 08:51:23 +00:00
|
|
|
|
(name "java-htsjdk")
|
2015-03-05 09:24:12 +00:00
|
|
|
|
(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\"")))))
|
2016-03-14 12:02:48 +00:00
|
|
|
|
(build-system ant-build-system)
|
2015-03-05 09:24:12 +00:00
|
|
|
|
(arguments
|
2016-03-14 12:02:48 +00:00
|
|
|
|
`(#:tests? #f ; test require Internet access
|
|
|
|
|
#:make-flags
|
|
|
|
|
(list (string-append "-Ddist=" (assoc-ref %outputs "out")
|
|
|
|
|
"/share/java/htsjdk/"))
|
|
|
|
|
#:build-target "all"
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
;; The build phase also installs the jars
|
|
|
|
|
(delete 'install))))
|
2015-03-05 09:24:12 +00:00
|
|
|
|
(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+)))
|
|
|
|
|
|
2015-12-18 16:40:02 +00:00
|
|
|
|
(define-public jellyfish
|
|
|
|
|
(package
|
|
|
|
|
(name "jellyfish")
|
|
|
|
|
(version "2.2.4")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/gmarcais/Jellyfish/"
|
|
|
|
|
"releases/download/v" version
|
|
|
|
|
"/jellyfish-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(outputs '("out" ;for library
|
|
|
|
|
"ruby" ;for Ruby bindings
|
|
|
|
|
"python")) ;for Python bindings
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags
|
|
|
|
|
(list (string-append "--enable-ruby-binding="
|
|
|
|
|
(assoc-ref %outputs "ruby"))
|
|
|
|
|
(string-append "--enable-python-binding="
|
|
|
|
|
(assoc-ref %outputs "python")))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'check 'set-SHELL-variable
|
|
|
|
|
(lambda _
|
|
|
|
|
;; generator_manager.hpp either uses /bin/sh or $SHELL
|
|
|
|
|
;; to run tests.
|
|
|
|
|
(setenv "SHELL" (which "bash"))
|
|
|
|
|
#t)))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("bc" ,bc)
|
|
|
|
|
("time" ,time)
|
|
|
|
|
("ruby" ,ruby)
|
|
|
|
|
("python" ,python-2)))
|
|
|
|
|
(synopsis "Tool for fast counting of k-mers in DNA")
|
|
|
|
|
(description
|
|
|
|
|
"Jellyfish is a tool for fast, memory-efficient counting of k-mers in
|
|
|
|
|
DNA. A k-mer is a substring of length k, and counting the occurrences of all
|
|
|
|
|
such substrings is a central step in many analyses of DNA sequence. Jellyfish
|
|
|
|
|
is a command-line program that reads FASTA and multi-FASTA files containing
|
|
|
|
|
DNA sequences. It outputs its k-mer counts in a binary format, which can be
|
|
|
|
|
translated into a human-readable text format using the @code{jellyfish dump}
|
|
|
|
|
command, or queried for specific k-mers with @code{jellyfish query}.")
|
|
|
|
|
(home-page "http://www.genome.umd.edu/jellyfish.html")
|
|
|
|
|
;; The combined work is published under the GPLv3 or later. Individual
|
|
|
|
|
;; files such as lib/jsoncpp.cpp are released under the Expat license.
|
|
|
|
|
(license (list license:gpl3+ license:expat))))
|
|
|
|
|
|
2015-02-26 16:10:39 +00:00
|
|
|
|
(define-public macs
|
|
|
|
|
(package
|
|
|
|
|
(name "macs")
|
2016-02-04 11:32:42 +00:00
|
|
|
|
(version "2.1.0.20151222")
|
2015-02-26 16:10:39 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-02-04 11:29:54 +00:00
|
|
|
|
(uri (pypi-uri "MACS2" version))
|
2015-02-26 16:10:39 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-02-04 11:32:42 +00:00
|
|
|
|
"1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
|
2015-02-26 16:10:39 +00:00
|
|
|
|
(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)))
|
|
|
|
|
|
2015-09-12 12:10:20 +00:00
|
|
|
|
(define-public mafft
|
|
|
|
|
(package
|
|
|
|
|
(name "mafft")
|
2015-12-15 10:34:52 +00:00
|
|
|
|
(version "7.267")
|
2015-09-12 12:10:20 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://mafft.cbrc.jp/alignment/software/mafft-" version
|
|
|
|
|
"-without-extensions-src.tgz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tgz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2015-12-15 10:34:52 +00:00
|
|
|
|
"1xl6xq1rfxkws0svrlhyqxhhwbv6r77jwblsdpcyiwzsscw6wlk0"))))
|
2015-09-12 12:10:20 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; no automated tests, though there are tests in the read me
|
|
|
|
|
#:make-flags (let ((out (assoc-ref %outputs "out")))
|
|
|
|
|
(list (string-append "PREFIX=" out)
|
|
|
|
|
(string-append "BINDIR="
|
|
|
|
|
(string-append out "/bin"))))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'enter-dir
|
|
|
|
|
(lambda _ (chdir "core") #t))
|
|
|
|
|
(add-after 'enter-dir 'patch-makefile
|
|
|
|
|
(lambda _
|
|
|
|
|
;; on advice from the MAFFT authors, there is no need to
|
|
|
|
|
;; distribute mafft-profile, mafft-distance, or
|
|
|
|
|
;; mafft-homologs.rb as they are too "specialised".
|
|
|
|
|
(substitute* "Makefile"
|
|
|
|
|
;; remove mafft-homologs.rb from SCRIPTS
|
|
|
|
|
(("^SCRIPTS = mafft mafft-homologs.rb")
|
|
|
|
|
"SCRIPTS = mafft")
|
2015-12-15 10:34:52 +00:00
|
|
|
|
;; remove mafft-homologs from MANPAGES
|
|
|
|
|
(("^MANPAGES = mafft.1 mafft-homologs.1")
|
|
|
|
|
"MANPAGES = mafft.1")
|
2015-09-12 12:10:20 +00:00
|
|
|
|
;; remove mafft-distance from PROGS
|
|
|
|
|
(("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
|
|
|
|
|
"PROGS = dvtditr dndfast7 dndblast sextet5")
|
|
|
|
|
;; remove mafft-profile from PROGS
|
|
|
|
|
(("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
|
|
|
|
|
"splittbfast disttbfast tbfast f2cl mccaskillwrap")
|
|
|
|
|
(("^rm -f mafft-profile mafft-profile.exe") "#")
|
|
|
|
|
(("^rm -f mafft-distance mafft-distance.exe") ")#")
|
|
|
|
|
;; do not install MAN pages in libexec folder
|
|
|
|
|
(("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
|
|
|
|
|
\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
|
|
|
|
|
#t))
|
2015-12-15 10:34:52 +00:00
|
|
|
|
(add-after 'enter-dir 'patch-paths
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(substitute* '("pairash.c"
|
|
|
|
|
"mafft.tmpl")
|
|
|
|
|
(("perl") (which "perl"))
|
|
|
|
|
(("([\"`| ])awk" _ prefix)
|
|
|
|
|
(string-append prefix (which "awk")))
|
|
|
|
|
(("grep") (which "grep")))
|
|
|
|
|
#t))
|
2015-09-12 12:10:20 +00:00
|
|
|
|
(delete 'configure))))
|
|
|
|
|
(inputs
|
2015-12-15 10:34:52 +00:00
|
|
|
|
`(("perl" ,perl)
|
|
|
|
|
("gawk" ,gawk)
|
|
|
|
|
("grep" ,grep)))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("coreutils" ,coreutils)))
|
2015-09-12 12:10:20 +00:00
|
|
|
|
(home-page "http://mafft.cbrc.jp/alignment/software/")
|
|
|
|
|
(synopsis "Multiple sequence alignment program")
|
|
|
|
|
(description
|
|
|
|
|
"MAFFT offers a range of multiple alignment methods for nucleotide and
|
|
|
|
|
protein sequences. For instance, it offers L-INS-i (accurate; for alignment
|
|
|
|
|
of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
|
|
|
|
|
sequences).")
|
|
|
|
|
(license (license:non-copyleft
|
|
|
|
|
"http://mafft.cbrc.jp/alignment/software/license.txt"
|
|
|
|
|
"BSD-3 with different formatting"))))
|
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)))
|
|
|
|
|
|
2016-01-16 12:12:23 +00:00
|
|
|
|
(define-public muscle
|
|
|
|
|
(package
|
|
|
|
|
(name "muscle")
|
|
|
|
|
(version "3.8.1551")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch/tarbomb)
|
|
|
|
|
(file-name (string-append name "-" version))
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://www.drive5.com/muscle/muscle_src_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:make-flags (list "LDLIBS = -lm")
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(replace 'check
|
|
|
|
|
;; There are no tests, so just test if it runs.
|
|
|
|
|
(lambda _ (zero? (system* "./muscle" "-version"))))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin")))
|
|
|
|
|
(install-file "muscle" bin)))))))
|
|
|
|
|
(home-page "http://www.drive5.com/muscle")
|
|
|
|
|
(synopsis "Multiple sequence alignment program")
|
|
|
|
|
(description
|
|
|
|
|
"MUSCLE aims to be a fast and accurate multiple sequence alignment
|
|
|
|
|
program for nucleotide and protein sequences.")
|
|
|
|
|
;; License information found in 'muscle -h' and usage.cpp.
|
|
|
|
|
(license license:public-domain)))
|
|
|
|
|
|
2015-06-09 14:10:51 +00:00
|
|
|
|
(define-public orfm
|
|
|
|
|
(package
|
|
|
|
|
(name "orfm")
|
2015-11-21 00:37:34 +00:00
|
|
|
|
(version "0.5.3")
|
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
|
2015-11-21 00:37:34 +00:00
|
|
|
|
"0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk"))))
|
2015-06-09 14:10:51 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs `(("zlib" ,zlib)))
|
2015-11-21 00:37:34 +00:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("ruby-bio-commandeer" ,ruby-bio-commandeer)
|
|
|
|
|
("ruby-rspec" ,ruby-rspec)
|
|
|
|
|
("ruby" ,ruby)))
|
2015-06-09 14:10:51 +00:00
|
|
|
|
(synopsis "Simple and not slow open reading frame (ORF) caller")
|
|
|
|
|
(description
|
2015-11-21 00:37:34 +00:00
|
|
|
|
"An ORF caller finds stretches of DNA that, when translated, are not
|
2015-06-09 14:10:51 +00:00
|
|
|
|
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")
|
2016-03-30 19:45:35 +00:00
|
|
|
|
(version "1.2.8")
|
2015-03-20 11:39:50 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-03-30 19:45:35 +00:00
|
|
|
|
(uri (pypi-uri "pbcore" version))
|
2015-03-20 11:39:50 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-03-30 19:45:35 +00:00
|
|
|
|
"02pfn5raa3zf739672bg0dkx7z3j2c4nx7vmpfjqy5b12jrqpymk"))))
|
2015-03-20 11:39:50 +00:00
|
|
|
|
(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
|
2016-03-30 19:45:35 +00:00
|
|
|
|
`(("python-docutils" ,python2-docutils)
|
|
|
|
|
("python-nose" ,python2-nose)
|
|
|
|
|
("python-setuptools" ,python2-setuptools)
|
|
|
|
|
("python-sphinx" ,python2-sphinx)))
|
2015-03-20 11:39:50 +00:00
|
|
|
|
(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
|
2015-10-28 13:39:13 +00:00
|
|
|
|
(let ((commit "8f5467fe6"))
|
2015-03-20 13:36:38 +00:00
|
|
|
|
(package
|
|
|
|
|
(name "pbtranscript-tofu")
|
2015-10-28 13:39:13 +00:00
|
|
|
|
(version (string-append "2.2.3." commit))
|
2015-03-20 13:36:38 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference
|
|
|
|
|
(url "https://github.com/PacificBiosciences/cDNA_primer.git")
|
|
|
|
|
(commit commit)))
|
2015-10-28 13:39:13 +00:00
|
|
|
|
(file-name (string-append name "-" version "-checkout"))
|
2015-03-20 13:36:38 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2015-10-28 13:39:13 +00:00
|
|
|
|
"1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; remove bundled Cython sources
|
|
|
|
|
(delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
|
|
|
|
|
#t))))
|
2015-03-20 13:36:38 +00:00
|
|
|
|
(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
|
2015-10-28 13:39:13 +00:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'enter-directory
|
|
|
|
|
(lambda _
|
|
|
|
|
(chdir "pbtranscript-tofu/pbtranscript/")
|
|
|
|
|
#t))
|
|
|
|
|
;; With setuptools version 18.0 and later this setup.py hack causes
|
|
|
|
|
;; a build error, so we disable it.
|
|
|
|
|
(add-after 'enter-directory 'patch-setuppy
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "setup.py"
|
|
|
|
|
(("if 'setuptools.extension' in sys.modules:")
|
|
|
|
|
"if False:"))
|
|
|
|
|
#t)))))
|
2015-03-20 13:36:38 +00:00
|
|
|
|
(inputs
|
2015-10-28 13:39:13 +00:00
|
|
|
|
`(("python-numpy" ,python2-numpy)
|
2015-03-20 13:36:38 +00:00
|
|
|
|
("python-bx-python" ,python2-bx-python)
|
2015-03-31 11:46:27 +00:00
|
|
|
|
("python-networkx" ,python2-networkx)
|
|
|
|
|
("python-scipy" ,python2-scipy)
|
2015-10-28 13:39:13 +00:00
|
|
|
|
("python-pbcore" ,python2-pbcore)
|
|
|
|
|
("python-h5py" ,python2-h5py)))
|
2015-03-20 13:36:38 +00:00
|
|
|
|
(native-inputs
|
2015-10-28 13:39:13 +00:00
|
|
|
|
`(("python-cython" ,python2-cython)
|
|
|
|
|
("python-nose" ,python2-nose)
|
2015-03-20 13:36:38 +00:00
|
|
|
|
("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))))
|
|
|
|
|
|
2016-03-11 16:01:00 +00:00
|
|
|
|
(define-public pyicoteo
|
|
|
|
|
(package
|
|
|
|
|
(name "pyicoteo")
|
|
|
|
|
(version "2.0.7")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
|
|
|
|
|
"pyicoteo/get/v" version ".tar.bz2"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.bz2"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:python ,python-2 ; does not work with Python 3
|
|
|
|
|
#:tests? #f)) ; there are no tests
|
|
|
|
|
(inputs
|
|
|
|
|
`(("python2-matplotlib" ,python2-matplotlib)))
|
|
|
|
|
(home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
|
|
|
|
|
(synopsis "Analyze high-throughput genetic sequencing data")
|
|
|
|
|
(description
|
|
|
|
|
"Pyicoteo is a suite of tools for the analysis of high-throughput genetic
|
|
|
|
|
sequencing data. It works with genomic coordinates. There are currently six
|
|
|
|
|
different command-line tools:
|
|
|
|
|
|
|
|
|
|
@enumerate
|
|
|
|
|
@item pyicoregion: for generating exploratory regions automatically;
|
|
|
|
|
@item pyicoenrich: for differential enrichment between two conditions;
|
|
|
|
|
@item pyicoclip: for calling CLIP-Seq peaks without a control;
|
|
|
|
|
@item pyicos: for genomic coordinates manipulation;
|
|
|
|
|
@item pyicoller: for peak calling on punctuated ChIP-Seq;
|
|
|
|
|
@item pyicount: to count how many reads from N experiment files overlap in a
|
|
|
|
|
region file;
|
|
|
|
|
@item pyicotrocol: to combine operations from pyicoteo.
|
|
|
|
|
@end enumerate\n")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2015-06-27 12:28:19 +00:00
|
|
|
|
(define-public prodigal
|
|
|
|
|
(package
|
|
|
|
|
(name "prodigal")
|
2016-02-15 21:17:39 +00:00
|
|
|
|
(version "2.6.3")
|
2015-06-27 12:28:19 +00:00
|
|
|
|
(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
|
2016-02-15 21:17:39 +00:00
|
|
|
|
"17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
|
2015-06-27 12:28:19 +00:00
|
|
|
|
(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"))
|
2016-04-08 12:18:13 +00:00
|
|
|
|
(patches (search-patches "rsem-makefile.patch"))
|
2015-05-21 13:43:25 +00:00
|
|
|
|
(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")
|
2016-04-23 23:45:07 +00:00
|
|
|
|
(version "1.3.1")
|
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
|
2016-04-23 23:45:07 +00:00
|
|
|
|
"0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"))))
|
2014-12-11 14:48:22 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2016-01-13 14:09:00 +00:00
|
|
|
|
`(#:modules ((ice-9 ftw)
|
2015-07-02 13:53:47 +00:00
|
|
|
|
(ice-9 regex)
|
|
|
|
|
(guix build gnu-build-system)
|
|
|
|
|
(guix build utils))
|
2016-01-13 14:09:00 +00:00
|
|
|
|
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
|
|
|
|
|
#:configure-flags (list "--with-ncurses")
|
2014-12-11 14:48:22 +00:00
|
|
|
|
#:phases
|
|
|
|
|
(alist-cons-after
|
2016-01-13 14:09:00 +00:00
|
|
|
|
'unpack 'patch-tests
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "test/test.pl"
|
|
|
|
|
;; The test script calls out to /bin/bash
|
|
|
|
|
(("/bin/bash") (which "bash")))
|
|
|
|
|
#t)
|
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))
|
2016-01-13 14:09:00 +00:00
|
|
|
|
%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
|
2016-01-16 14:48:51 +00:00
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
|
,@(substitute-keyword-arguments (package-arguments samtools)
|
|
|
|
|
((#:make-flags flags)
|
|
|
|
|
`(cons "LIBCURSES=-lncurses" ,flags))
|
|
|
|
|
((#: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)
|
|
|
|
|
(delete 'configure))))))))
|
2015-04-28 09:28:16 +00:00
|
|
|
|
|
2015-10-16 15:41:07 +00:00
|
|
|
|
(define-public mosaik
|
|
|
|
|
(let ((commit "5c25216d"))
|
|
|
|
|
(package
|
|
|
|
|
(name "mosaik")
|
|
|
|
|
(version "2.2.30")
|
|
|
|
|
(source (origin
|
|
|
|
|
;; There are no release tarballs nor tags.
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference
|
|
|
|
|
(url "https://github.com/wanpinglee/MOSAIK.git")
|
|
|
|
|
(commit commit)))
|
|
|
|
|
(file-name (string-append name "-" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; no tests
|
|
|
|
|
#:make-flags (list "CC=gcc")
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(replace 'configure
|
|
|
|
|
(lambda _ (chdir "src") #t))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out")
|
|
|
|
|
"/bin")))
|
|
|
|
|
(mkdir-p bin)
|
|
|
|
|
(copy-recursively "../bin" bin)
|
|
|
|
|
#t))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("perl" ,perl)
|
|
|
|
|
("zlib" ,zlib)))
|
2015-10-23 08:35:00 +00:00
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-10-16 15:41:07 +00:00
|
|
|
|
(home-page "https://code.google.com/p/mosaik-aligner/")
|
|
|
|
|
(synopsis "Map nucleotide sequence reads to reference genomes")
|
|
|
|
|
(description
|
|
|
|
|
"MOSAIK is a program for mapping second and third-generation sequencing
|
|
|
|
|
reads to a reference genome. MOSAIK can align reads generated by all the
|
|
|
|
|
major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
|
|
|
|
|
Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
|
|
|
|
|
;; MOSAIK is released under the GPLv2+ with the exception of third-party
|
|
|
|
|
;; code released into the public domain:
|
|
|
|
|
;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
|
|
|
|
|
;; 2. MD5 implementation - RSA Data Security, RFC 1321
|
|
|
|
|
(license (list license:gpl2+ license:public-domain)))))
|
|
|
|
|
|
2015-04-14 12:23:19 +00:00
|
|
|
|
(define-public ngs-sdk
|
|
|
|
|
(package
|
|
|
|
|
(name "ngs-sdk")
|
2016-01-26 00:40:26 +00:00
|
|
|
|
(version "1.2.3")
|
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
|
2016-01-26 00:40:26 +00:00
|
|
|
|
"15074fdi94c6pjy83hhk22r86kfvzpaz2i07h3rqg9yy6x3w0pk2"))))
|
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)))
|
2015-10-17 20:42:13 +00:00
|
|
|
|
;; According to the test
|
|
|
|
|
;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
|
|
|
|
|
;; in ngs-sdk/setup/konfigure.perl
|
2015-10-17 20:51:12 +00:00
|
|
|
|
(supported-systems '("i686-linux" "x86_64-linux"))
|
2015-04-14 12:23:19 +00:00
|
|
|
|
(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)))
|
|
|
|
|
|
2016-04-16 08:51:23 +00:00
|
|
|
|
(define-public java-ngs
|
2015-04-14 12:24:01 +00:00
|
|
|
|
(package (inherit ngs-sdk)
|
2016-04-16 08:51:23 +00:00
|
|
|
|
(name "java-ngs")
|
2015-04-14 12:24:01 +00:00
|
|
|
|
(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)
|
2015-11-20 14:14:55 +00:00
|
|
|
|
`(modify-phases ,phases
|
|
|
|
|
(replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
|
2015-04-14 12:24:01 +00:00
|
|
|
|
(inputs
|
2015-12-30 13:25:09 +00:00
|
|
|
|
`(("jdk" ,icedtea "jdk")
|
2015-04-14 12:24:01 +00:00
|
|
|
|
("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")
|
2016-01-26 00:45:10 +00:00
|
|
|
|
(version "2.5.7")
|
2015-04-14 12:42:49 +00:00
|
|
|
|
(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
|
2016-01-26 00:45:10 +00:00
|
|
|
|
"0hay5hy8ynva3mi5wbn4wmq1q23qwxc3aqzbb86hg3x4f1r73270"))))
|
2015-04-14 12:42:49 +00:00
|
|
|
|
(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")))
|
|
|
|
|
;; 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="
|
2016-04-16 08:51:23 +00:00
|
|
|
|
(assoc-ref inputs "java-ngs"))
|
2015-04-14 12:42:49 +00:00
|
|
|
|
(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)
|
2016-04-16 08:51:23 +00:00
|
|
|
|
("java-ngs" ,java-ngs)
|
2015-04-14 12:42:49 +00:00
|
|
|
|
("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"))
|
2016-04-08 12:18:13 +00:00
|
|
|
|
(patches (search-patches "plink-1.07-unclobber-i.patch"))))
|
2015-06-25 10:04:05 +00:00
|
|
|
|
(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+))))
|
|
|
|
|
|
2015-11-20 10:14:00 +00:00
|
|
|
|
(define-public smithlab-cpp
|
|
|
|
|
(let ((revision "1")
|
|
|
|
|
(commit "728a097"))
|
|
|
|
|
(package
|
|
|
|
|
(name "smithlab-cpp")
|
|
|
|
|
(version (string-append "0." revision "." commit))
|
|
|
|
|
(source (origin
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference
|
|
|
|
|
(url "https://github.com/smithlabcode/smithlab_cpp.git")
|
|
|
|
|
(commit commit)))
|
|
|
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:modules ((guix build gnu-build-system)
|
|
|
|
|
(guix build utils)
|
|
|
|
|
(srfi srfi-26))
|
|
|
|
|
#:tests? #f ;no "check" target
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'use-samtools-headers
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* '("SAM.cpp"
|
|
|
|
|
"SAM.hpp")
|
|
|
|
|
(("sam.h") "samtools/sam.h"))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(lib (string-append out "/lib"))
|
|
|
|
|
(include (string-append out "/include/smithlab-cpp")))
|
|
|
|
|
(mkdir-p lib)
|
|
|
|
|
(mkdir-p include)
|
|
|
|
|
(for-each (cut install-file <> lib)
|
|
|
|
|
(find-files "." "\\.o$"))
|
|
|
|
|
(for-each (cut install-file <> include)
|
|
|
|
|
(find-files "." "\\.hpp$")))
|
|
|
|
|
#t))
|
|
|
|
|
(delete 'configure))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("samtools" ,samtools-0.1)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(home-page "https://github.com/smithlabcode/smithlab_cpp")
|
|
|
|
|
(synopsis "C++ helper library for functions used in Smith lab projects")
|
|
|
|
|
(description
|
|
|
|
|
"Smithlab CPP is a C++ library that includes functions used in many of
|
|
|
|
|
the Smith lab bioinformatics projects, such as a wrapper around Samtools data
|
|
|
|
|
structures, classes for genomic regions, mapped sequencing reads, etc.")
|
|
|
|
|
(license license:gpl3+))))
|
|
|
|
|
|
2015-06-23 08:54:00 +00:00
|
|
|
|
(define-public preseq
|
|
|
|
|
(package
|
|
|
|
|
(name "preseq")
|
2015-11-20 10:14:48 +00:00
|
|
|
|
(version "2.0")
|
2015-06-23 08:54:00 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2015-11-20 10:14:48 +00:00
|
|
|
|
(uri (string-append "https://github.com/smithlabcode/"
|
|
|
|
|
"preseq/archive/v" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
2015-06-23 08:54:00 +00:00
|
|
|
|
(sha256
|
2015-11-20 10:14:48 +00:00
|
|
|
|
(base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
|
2015-06-23 08:54:00 +00:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Remove bundled samtools.
|
2015-11-20 10:14:48 +00:00
|
|
|
|
'(delete-file-recursively "samtools"))))
|
2015-06-23 08:54:00 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure))
|
2015-11-20 10:14:48 +00:00
|
|
|
|
#:make-flags
|
|
|
|
|
(list (string-append "PREFIX="
|
|
|
|
|
(assoc-ref %outputs "out"))
|
|
|
|
|
(string-append "LIBBAM="
|
|
|
|
|
(assoc-ref %build-inputs "samtools")
|
|
|
|
|
"/lib/libbam.a")
|
|
|
|
|
(string-append "SMITHLAB_CPP="
|
|
|
|
|
(assoc-ref %build-inputs "smithlab-cpp")
|
|
|
|
|
"/lib")
|
|
|
|
|
"PROGS=preseq"
|
|
|
|
|
"INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
|
2015-06-23 08:54:00 +00:00
|
|
|
|
(inputs
|
|
|
|
|
`(("gsl" ,gsl)
|
|
|
|
|
("samtools" ,samtools-0.1)
|
2015-11-20 10:14:48 +00:00
|
|
|
|
("smithlab-cpp" ,smithlab-cpp)
|
2015-06-23 08:54:00 +00:00
|
|
|
|
("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")
|
2016-01-26 00:48:21 +00:00
|
|
|
|
(version "2.5.7")
|
2015-04-14 12:43:32 +00:00
|
|
|
|
(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
|
2016-01-26 00:48:21 +00:00
|
|
|
|
"0q93qg744x787d08qmjmdafki1wkbvkdwynayjnjd454gkd26jl5"))))
|
2015-04-14 12:43:32 +00:00
|
|
|
|
(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)))
|
|
|
|
|
|
2015-02-06 11:38:40 +00:00
|
|
|
|
(define-public seqan
|
|
|
|
|
(package
|
|
|
|
|
(name "seqan")
|
|
|
|
|
(version "1.4.2")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://packages.seqan.de/seqan-library/"
|
|
|
|
|
"seqan-library-" version ".tar.bz2"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
|
|
|
|
|
;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
|
|
|
|
|
;; makes sense to split the outputs.
|
|
|
|
|
(outputs '("out" "doc"))
|
|
|
|
|
(build-system trivial-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:modules ((guix build utils))
|
|
|
|
|
#:builder
|
|
|
|
|
(begin
|
|
|
|
|
(use-modules (guix build utils))
|
|
|
|
|
(let ((tar (assoc-ref %build-inputs "tar"))
|
|
|
|
|
(bzip (assoc-ref %build-inputs "bzip2"))
|
|
|
|
|
(out (assoc-ref %outputs "out"))
|
|
|
|
|
(doc (assoc-ref %outputs "doc")))
|
|
|
|
|
(setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
|
|
|
|
|
(system* "tar" "xvf" (assoc-ref %build-inputs "source"))
|
|
|
|
|
(chdir (string-append "seqan-library-" ,version))
|
|
|
|
|
(copy-recursively "include" (string-append out "/include"))
|
|
|
|
|
(copy-recursively "share" (string-append doc "/share"))))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("source" ,source)
|
|
|
|
|
("tar" ,tar)
|
|
|
|
|
("bzip2" ,bzip2)))
|
|
|
|
|
(home-page "http://www.seqan.de")
|
|
|
|
|
(synopsis "Library for nucleotide sequence analysis")
|
|
|
|
|
(description
|
|
|
|
|
"SeqAn is a C++ library of efficient algorithms and data structures for
|
|
|
|
|
the analysis of sequences with the focus on biological data. It contains
|
|
|
|
|
algorithms and data structures for string representation and their
|
|
|
|
|
manipulation, online and indexed string search, efficient I/O of
|
|
|
|
|
bioinformatics file formats, sequence alignment, and more.")
|
|
|
|
|
(license license:bsd-3)))
|
2015-02-09 14:38:30 +00:00
|
|
|
|
|
2015-09-19 09:31:57 +00:00
|
|
|
|
(define-public seqmagick
|
|
|
|
|
(package
|
|
|
|
|
(name "seqmagick")
|
|
|
|
|
(version "0.6.1")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://pypi.python.org/packages/source/s/seqmagick/seqmagick-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
|
|
|
|
|
`(#:python ,python-2
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
;; Current test in setup.py does not work as of 0.6.1,
|
|
|
|
|
;; so use nose to run tests instead for now. See
|
|
|
|
|
;; https://github.com/fhcrc/seqmagick/issues/55
|
|
|
|
|
(replace 'check (lambda _ (zero? (system* "nosetests")))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("python-biopython" ,python2-biopython)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python-setuptools" ,python2-setuptools)
|
|
|
|
|
("python-nose" ,python2-nose)))
|
|
|
|
|
(home-page "http://github.com/fhcrc/seqmagick")
|
|
|
|
|
(synopsis "Tools for converting and modifying sequence files")
|
|
|
|
|
(description
|
|
|
|
|
"Bioinformaticians often have to convert sequence files between formats
|
|
|
|
|
and do little manipulations on them, and it's not worth writing scripts for
|
|
|
|
|
that. Seqmagick is a utility to expose the file format conversion in
|
|
|
|
|
BioPython in a convenient way. Instead of having a big mess of scripts, there
|
|
|
|
|
is one that takes arguments.")
|
|
|
|
|
(license license:gpl3)))
|
|
|
|
|
|
2015-12-10 10:56:52 +00:00
|
|
|
|
(define-public snap-aligner
|
|
|
|
|
(package
|
|
|
|
|
(name "snap-aligner")
|
|
|
|
|
(version "1.0beta.18")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/amplab/snap/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(replace 'check (lambda _ (zero? (system* "./unit_tests"))))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin")))
|
|
|
|
|
(mkdir-p bin)
|
|
|
|
|
(install-file "snap-aligner" bin)
|
|
|
|
|
(install-file "SNAPCommand" bin)
|
|
|
|
|
#t))))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
|
(home-page "http://snap.cs.berkeley.edu/")
|
|
|
|
|
(synopsis "Short read DNA sequence aligner")
|
|
|
|
|
(description
|
|
|
|
|
"SNAP is a fast and accurate aligner for short DNA reads. It is
|
|
|
|
|
optimized for modern read lengths of 100 bases or higher, and takes advantage
|
|
|
|
|
of these reads to align data quickly through a hash-based indexing scheme.")
|
|
|
|
|
(license license:asl2.0)))
|
|
|
|
|
|
2016-01-16 03:33:08 +00:00
|
|
|
|
(define-public sortmerna
|
|
|
|
|
(package
|
|
|
|
|
(name "sortmerna")
|
2016-02-02 12:39:05 +00:00
|
|
|
|
(version "2.1")
|
2016-01-16 03:33:08 +00:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/biocore/sortmerna/archive/"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-02-02 12:39:05 +00:00
|
|
|
|
"1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4"))))
|
2016-01-16 03:33:08 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(outputs '("out" ;for binaries
|
|
|
|
|
"db")) ;for sequence databases
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin"))
|
|
|
|
|
(db (assoc-ref outputs "db"))
|
|
|
|
|
(share
|
|
|
|
|
(string-append db "/share/sortmerna/rRNA_databases")))
|
|
|
|
|
(install-file "sortmerna" bin)
|
|
|
|
|
(install-file "indexdb_rna" bin)
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(install-file file share))
|
|
|
|
|
(find-files "rRNA_databases" ".*fasta"))
|
|
|
|
|
#t))))))
|
|
|
|
|
(home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
|
|
|
|
|
(synopsis "Biological sequence analysis tool for NGS reads")
|
|
|
|
|
(description
|
|
|
|
|
"SortMeRNA is a biological sequence analysis tool for filtering, mapping
|
|
|
|
|
and operational taxonomic unit (OTU) picking of next generation
|
|
|
|
|
sequencing (NGS) reads. The core algorithm is based on approximate seeds and
|
|
|
|
|
allows for fast and sensitive analyses of nucleotide sequences. The main
|
|
|
|
|
application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
|
|
|
|
|
(license license:lgpl3)))
|
|
|
|
|
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(define-public star
|
|
|
|
|
(package
|
|
|
|
|
(name "star")
|
2016-01-19 15:26:47 +00:00
|
|
|
|
(version "2.5.1b")
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-01-19 15:26:47 +00:00
|
|
|
|
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-01-19 15:26:47 +00:00
|
|
|
|
"0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4"))
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
2016-01-19 15:26:47 +00:00
|
|
|
|
'(begin
|
|
|
|
|
(substitute* "source/Makefile"
|
|
|
|
|
(("/bin/rm") "rm"))
|
|
|
|
|
;; Remove pre-built binaries and bundled htslib sources.
|
|
|
|
|
(delete-file-recursively "bin/MacOSX_x86_64")
|
|
|
|
|
(delete-file-recursively "bin/Linux_x86_64")
|
|
|
|
|
(delete-file-recursively "source/htslib")
|
|
|
|
|
#t))))
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:tests? #f ;no check target
|
|
|
|
|
#:make-flags '("STAR")
|
|
|
|
|
#:phases
|
2016-01-19 15:04:01 +00:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'enter-source-dir
|
|
|
|
|
(lambda _ (chdir "source") #t))
|
2016-01-19 15:26:47 +00:00
|
|
|
|
(add-after 'enter-source-dir 'do-not-use-bundled-htslib
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "Makefile"
|
|
|
|
|
(("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
|
|
|
|
|
_ prefix) prefix))
|
|
|
|
|
(substitute* '("BAMfunctions.cpp"
|
|
|
|
|
"signalFromBAM.h"
|
|
|
|
|
"bam_cat.h"
|
|
|
|
|
"bam_cat.c"
|
|
|
|
|
"STAR.cpp"
|
|
|
|
|
"bamRemoveDuplicates.cpp")
|
|
|
|
|
(("#include \"htslib/([^\"]+\\.h)\"" _ header)
|
|
|
|
|
(string-append "#include <" header ">")))
|
|
|
|
|
(substitute* "IncludeDefine.h"
|
|
|
|
|
(("\"htslib/(htslib/[^\"]+.h)\"" _ header)
|
|
|
|
|
(string-append "<" header ">")))
|
|
|
|
|
#t))
|
2016-01-19 15:04:01 +00:00
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
|
|
|
(install-file "STAR" bin))
|
|
|
|
|
#t))
|
|
|
|
|
(delete 'configure))))
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("vim" ,vim))) ; for xxd
|
|
|
|
|
(inputs
|
2016-01-19 15:26:47 +00:00
|
|
|
|
`(("htslib" ,htslib)
|
|
|
|
|
("zlib" ,zlib)))
|
2015-02-09 14:38:30 +00:00
|
|
|
|
(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
|
2015-10-23 12:16:27 +00:00
|
|
|
|
;; The CC and CCFLAGS variables are set to contain a lot of x86_64
|
|
|
|
|
;; optimizations by default, so we override these flags such that x86_64
|
|
|
|
|
;; flags are only added when the build target is an x86_64 system.
|
|
|
|
|
#:make-flags
|
|
|
|
|
(list (let ((system ,(or (%current-target-system)
|
|
|
|
|
(%current-system)))
|
|
|
|
|
(flags '("-ggdb" "-fomit-frame-pointer"
|
|
|
|
|
"-ffast-math" "-funroll-loops"
|
|
|
|
|
"-fmessage-length=0"
|
|
|
|
|
"-O9" "-Wall" "-DMAKE_FOR_EXON"
|
|
|
|
|
"-DMAKE_STANDALONE"
|
|
|
|
|
"-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
|
|
|
|
|
(flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
|
|
|
|
|
(if (string-prefix? "x86_64" system)
|
|
|
|
|
(string-append "CCFLAGS=" (string-join (append flags flags64)))
|
|
|
|
|
(string-append "CCFLAGS=" (string-join flags))))
|
|
|
|
|
"-f" "Makefile.Linux"
|
|
|
|
|
"CC=gcc ${CCFLAGS}")
|
2015-04-16 09:19:45 +00:00
|
|
|
|
#: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+)))
|
|
|
|
|
|
2016-02-02 14:45:38 +00:00
|
|
|
|
(define-public stringtie
|
|
|
|
|
(package
|
|
|
|
|
(name "stringtie")
|
|
|
|
|
(version "1.2.1")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
|
|
|
|
|
"stringtie-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
(delete-file-recursively "samtools-0.1.18")
|
|
|
|
|
#t))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ;no test suite
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
;; no configure script
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(add-before 'build 'use-system-samtools
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "Makefile"
|
|
|
|
|
(("stringtie: \\$\\{BAM\\}/libbam\\.a")
|
|
|
|
|
"stringtie: "))
|
|
|
|
|
(substitute* '("gclib/GBam.h"
|
|
|
|
|
"gclib/GBam.cpp")
|
|
|
|
|
(("#include \"(bam|sam|kstring).h\"" _ header)
|
|
|
|
|
(string-append "#include <samtools/" header ".h>")))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
|
|
|
|
(install-file "stringtie" bin)
|
|
|
|
|
#t))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("samtools" ,samtools-0.1)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(home-page "http://ccb.jhu.edu/software/stringtie/")
|
|
|
|
|
(synopsis "Transcript assembly and quantification for RNA-Seq data")
|
|
|
|
|
(description
|
|
|
|
|
"StringTie is a fast and efficient assembler of RNA-Seq sequence
|
|
|
|
|
alignments into potential transcripts. It uses a novel network flow algorithm
|
|
|
|
|
as well as an optional de novo assembly step to assemble and quantitate
|
|
|
|
|
full-length transcripts representing multiple splice variants for each gene
|
|
|
|
|
locus. Its input can include not only the alignments of raw reads used by
|
|
|
|
|
other transcript assemblers, but also alignments of longer sequences that have
|
|
|
|
|
been assembled from those reads. To identify differentially expressed genes
|
|
|
|
|
between experiments, StringTie's output can be processed either by the
|
|
|
|
|
Cuffdiff or Ballgown programs.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(define-public vcftools
|
|
|
|
|
(package
|
|
|
|
|
(name "vcftools")
|
2016-04-04 18:04:48 +00:00
|
|
|
|
(version "0.1.14")
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
2016-04-04 18:04:48 +00:00
|
|
|
|
"https://github.com/vcftools/vcftools/releases/download/v"
|
|
|
|
|
version "/vcftools-" version ".tar.gz"))
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-04-04 18:04:48 +00:00
|
|
|
|
"10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(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")
|
2016-04-04 18:04:48 +00:00
|
|
|
|
"/share/man/man1"))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("pkg-config" ,pkg-config)))
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(inputs
|
|
|
|
|
`(("perl" ,perl)
|
|
|
|
|
("zlib" ,zlib)))
|
2016-04-04 18:04:48 +00:00
|
|
|
|
(home-page "https://vcftools.github.io/")
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(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
|
2016-04-04 18:04:48 +00:00
|
|
|
|
;; at https://vcftools.github.io/license.html
|
2015-03-20 15:50:33 +00:00
|
|
|
|
(license license:lgpl3)))
|
2015-09-14 14:32:27 +00:00
|
|
|
|
|
2015-09-30 08:35:32 +00:00
|
|
|
|
(define-public vsearch
|
|
|
|
|
(package
|
|
|
|
|
(name "vsearch")
|
2016-02-15 12:22:01 +00:00
|
|
|
|
(version "1.10.0")
|
2015-09-30 08:35:32 +00:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/torognes/vsearch/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-02-15 12:22:01 +00:00
|
|
|
|
"1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5"))
|
2015-09-30 08:35:32 +00:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; Remove bundled cityhash and '-mtune=native'.
|
|
|
|
|
(substitute* "src/Makefile.am"
|
|
|
|
|
(("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \
|
|
|
|
|
-O3 -mtune=native -Wall -Wsign-compare")
|
|
|
|
|
(string-append "AM_CXXFLAGS=-lcityhash"
|
|
|
|
|
" -O3 -Wall -Wsign-compare"))
|
2016-02-15 12:22:01 +00:00
|
|
|
|
(("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\")
|
2015-09-30 08:35:32 +00:00
|
|
|
|
"__top_builddir__bin_vsearch_SOURCES = \\")
|
2016-02-15 12:22:01 +00:00
|
|
|
|
(("^city.h \\\\") "\\")
|
|
|
|
|
(("^citycrc.h \\\\") "\\")
|
|
|
|
|
(("^libcityhash_a.*") "")
|
|
|
|
|
(("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \
|
|
|
|
|
libcityhash.a")
|
|
|
|
|
"noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a")
|
|
|
|
|
(("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
|
|
|
|
|
libcpu_sse2.a libcityhash.a")
|
|
|
|
|
"__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
|
|
|
|
|
libcpu_sse2.a -lcityhash"))
|
2015-09-30 08:35:32 +00:00
|
|
|
|
(substitute* "src/vsearch.h"
|
2016-02-15 12:22:01 +00:00
|
|
|
|
(("^\\#include \"city.h\"") "#include <city.h>")
|
|
|
|
|
(("^\\#include \"citycrc.h\"") "#include <citycrc.h>"))
|
|
|
|
|
(delete-file "src/city.h")
|
|
|
|
|
(delete-file "src/citycrc.h")
|
|
|
|
|
(delete-file "src/city.cc")
|
2015-09-30 08:35:32 +00:00
|
|
|
|
#t))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'autogen
|
|
|
|
|
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)
|
|
|
|
|
("bzip2" ,bzip2)
|
|
|
|
|
("cityhash" ,cityhash)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("autoconf" ,autoconf)
|
|
|
|
|
("automake" ,automake)))
|
|
|
|
|
(synopsis "Sequence search tools for metagenomics")
|
|
|
|
|
(description
|
|
|
|
|
"VSEARCH supports DNA sequence searching, clustering, chimera detection,
|
|
|
|
|
dereplication, pairwise alignment, shuffling, subsampling, sorting and
|
|
|
|
|
masking. The tool takes advantage of parallelism in the form of SIMD
|
|
|
|
|
vectorization as well as multiple threads to perform accurate alignments at
|
|
|
|
|
high speed. VSEARCH uses an optimal global aligner (full dynamic programming
|
|
|
|
|
Needleman-Wunsch).")
|
|
|
|
|
(home-page "https://github.com/torognes/vsearch")
|
2015-10-03 01:46:22 +00:00
|
|
|
|
;; vsearch uses non-portable SSE intrinsics so building fails on other
|
|
|
|
|
;; platforms.
|
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-09-30 08:35:32 +00:00
|
|
|
|
;; Dual licensed; also includes public domain source.
|
|
|
|
|
(license (list license:gpl3 license:bsd-2))))
|
|
|
|
|
|
2015-09-14 14:32:27 +00:00
|
|
|
|
(define-public bio-locus
|
|
|
|
|
(package
|
|
|
|
|
(name "bio-locus")
|
|
|
|
|
(version "0.0.7")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (rubygems-uri "bio-locus" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
|
|
|
|
|
(build-system ruby-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("ruby-rspec" ,ruby-rspec)))
|
|
|
|
|
(synopsis "Tool for fast querying of genome locations")
|
|
|
|
|
(description
|
|
|
|
|
"Bio-locus is a tabix-like tool for fast querying of genome
|
|
|
|
|
locations. Many file formats in bioinformatics contain records that
|
|
|
|
|
start with a chromosome name and a position for a SNP, or a start-end
|
|
|
|
|
position for indels. Bio-locus allows users to store this chr+pos or
|
|
|
|
|
chr+pos+alt information in a database.")
|
|
|
|
|
(home-page "https://github.com/pjotrp/bio-locus")
|
|
|
|
|
(license license:expat)))
|
2015-09-17 06:17:44 +00:00
|
|
|
|
|
2015-09-28 10:19:21 +00:00
|
|
|
|
(define-public bio-blastxmlparser
|
|
|
|
|
(package
|
|
|
|
|
(name "bio-blastxmlparser")
|
|
|
|
|
(version "2.0.4")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (rubygems-uri "bio-blastxmlparser" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
|
|
|
|
|
(build-system ruby-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("ruby-bio-logger" ,ruby-bio-logger)
|
|
|
|
|
("ruby-nokogiri" ,ruby-nokogiri)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("ruby-rspec" ,ruby-rspec)))
|
|
|
|
|
(synopsis "Fast big data BLAST XML parser and library")
|
|
|
|
|
(description
|
|
|
|
|
"Very fast parallel big-data BLAST XML file parser which can be used as
|
|
|
|
|
command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
|
|
|
|
|
generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
|
|
|
|
|
(home-page "http://github.com/pjotrp/blastxmlparser")
|
|
|
|
|
(license license:expat)))
|
|
|
|
|
|
2015-09-17 06:17:44 +00:00
|
|
|
|
(define-public bioruby
|
|
|
|
|
(package
|
|
|
|
|
(name "bioruby")
|
|
|
|
|
(version "1.5.0")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (rubygems-uri "bio" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
|
|
|
|
|
(build-system ruby-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("ruby-libxml" ,ruby-libxml)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("which" ,which))) ; required for test phase
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'build 'patch-test-command
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* '("test/functional/bio/test_command.rb")
|
|
|
|
|
(("/bin/sh") (which "sh")))
|
|
|
|
|
(substitute* '("test/functional/bio/test_command.rb")
|
|
|
|
|
(("/bin/ls") (which "ls")))
|
|
|
|
|
(substitute* '("test/functional/bio/test_command.rb")
|
|
|
|
|
(("which") (which "which")))
|
|
|
|
|
(substitute* '("test/functional/bio/test_command.rb",
|
|
|
|
|
"test/data/command/echoarg2.sh")
|
|
|
|
|
(("/bin/echo") (which "echo")))
|
|
|
|
|
#t)))))
|
|
|
|
|
(synopsis "Ruby library, shell and utilities for bioinformatics")
|
|
|
|
|
(description "BioRuby comes with a comprehensive set of Ruby development
|
|
|
|
|
tools and libraries for bioinformatics and molecular biology. BioRuby has
|
|
|
|
|
components for sequence analysis, pathway analysis, protein modelling and
|
|
|
|
|
phylogenetic analysis; it supports many widely used data formats and provides
|
|
|
|
|
easy access to databases, external programs and public web services, including
|
|
|
|
|
BLAST, KEGG, GenBank, MEDLINE and GO.")
|
|
|
|
|
(home-page "http://bioruby.org/")
|
|
|
|
|
;; Code is released under Ruby license, except for setup
|
|
|
|
|
;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
|
|
|
|
|
(license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
|
2015-09-19 22:32:45 +00:00
|
|
|
|
|
2015-12-17 15:51:28 +00:00
|
|
|
|
(define-public r-acsnminer
|
|
|
|
|
(package
|
|
|
|
|
(name "r-acsnminer")
|
2016-04-19 15:46:27 +00:00
|
|
|
|
(version "0.16.01.29")
|
2015-12-17 15:51:28 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "ACSNMineR" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-04-19 15:46:27 +00:00
|
|
|
|
"1b1243wkncanm1blkqzicjgzb576vzcg4iwinsgn2xqr7f264amf"))))
|
2015-12-17 15:51:28 +00:00
|
|
|
|
(properties `((upstream-name . "ACSNMineR")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
|
|
|
("r-gridextra" ,r-gridextra)))
|
|
|
|
|
(home-page "http://cran.r-project.org/web/packages/ACSNMineR")
|
|
|
|
|
(synopsis "Gene enrichment analysis")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides tools to compute and represent gene set enrichment
|
|
|
|
|
or depletion from your data based on pre-saved maps from the @dfn{Atlas of
|
|
|
|
|
Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
|
|
|
|
|
enrichment can be run with hypergeometric test or Fisher exact test, and can
|
|
|
|
|
use multiple corrections. Visualization of data can be done either by
|
|
|
|
|
barplots or heatmaps.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2015-12-18 11:06:55 +00:00
|
|
|
|
(define-public r-biocgenerics
|
|
|
|
|
(package
|
|
|
|
|
(name "r-biocgenerics")
|
2016-05-10 09:43:43 +00:00
|
|
|
|
(version "0.18.0")
|
2015-12-18 11:06:55 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "BiocGenerics" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:43:43 +00:00
|
|
|
|
"1jjp48vbph09w5bmc7368gjjywsa1lmzfybpiwlypr60b51vlkp6"))))
|
2015-12-18 11:06:55 +00:00
|
|
|
|
(properties
|
2016-01-07 15:44:47 +00:00
|
|
|
|
`((upstream-name . "BiocGenerics")))
|
2015-12-18 11:06:55 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(home-page "http://bioconductor.org/packages/BiocGenerics")
|
|
|
|
|
(synopsis "S4 generic functions for Bioconductor")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides S4 generic functions needed by many Bioconductor
|
|
|
|
|
packages.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-16 09:27:48 +00:00
|
|
|
|
(define-public r-dnacopy
|
|
|
|
|
(package
|
|
|
|
|
(name "r-dnacopy")
|
2016-05-10 09:45:29 +00:00
|
|
|
|
(version "1.46.0")
|
2016-03-16 09:27:48 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "DNAcopy" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:45:29 +00:00
|
|
|
|
"0vwv2mndfjpcjp4sybg75abc7xnx8zyw8zjk717k6xh8c33ymcip"))))
|
2016-03-16 09:27:48 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "DNAcopy")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
2016-03-18 22:00:04 +00:00
|
|
|
|
(home-page "https://bioconductor.org/packages/DNAcopy")
|
2016-03-16 09:27:48 +00:00
|
|
|
|
(synopsis "Implementation of a circular binary segmentation algorithm")
|
|
|
|
|
(description "This package implements the circular binary segmentation (CBS)
|
|
|
|
|
algorithm to segment DNA copy number data and identify genomic regions with
|
|
|
|
|
abnormal copy number.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2015-12-18 11:07:18 +00:00
|
|
|
|
(define-public r-s4vectors
|
|
|
|
|
(package
|
|
|
|
|
(name "r-s4vectors")
|
2016-05-10 09:46:15 +00:00
|
|
|
|
(version "0.10.0")
|
2015-12-18 11:07:18 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "S4Vectors" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:46:15 +00:00
|
|
|
|
"1mi6lf6pnb9l657igy0vj4yz03yawbr2jhk22l757fzbjc7n9q3b"))))
|
2015-12-18 11:07:18 +00:00
|
|
|
|
(properties
|
2016-01-07 15:44:47 +00:00
|
|
|
|
`((upstream-name . "S4Vectors")))
|
2015-12-18 11:07:18 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/S4Vectors")
|
|
|
|
|
(synopsis "S4 implementation of vectors and lists")
|
|
|
|
|
(description
|
|
|
|
|
"The S4Vectors package defines the @code{Vector} and @code{List} virtual
|
|
|
|
|
classes and a set of generic functions that extend the semantic of ordinary
|
|
|
|
|
vectors and lists in R. Package developers can easily implement vector-like
|
|
|
|
|
or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
|
|
|
|
|
In addition, a few low-level concrete subclasses of general interest (e.g.
|
|
|
|
|
@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
|
|
|
|
|
S4Vectors package itself.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 11:07:39 +00:00
|
|
|
|
(define-public r-iranges
|
|
|
|
|
(package
|
|
|
|
|
(name "r-iranges")
|
2016-05-10 09:47:03 +00:00
|
|
|
|
(version "2.6.0")
|
2015-12-18 11:07:39 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "IRanges" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:47:03 +00:00
|
|
|
|
"0dz7z0pk8hq79mcgylw920999s08h6j8xrl31rdxhssmi7l8v6vy"))))
|
2015-12-18 11:07:39 +00:00
|
|
|
|
(properties
|
2016-01-07 15:44:47 +00:00
|
|
|
|
`((upstream-name . "IRanges")))
|
2015-12-18 11:07:39 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/IRanges")
|
|
|
|
|
(synopsis "Infrastructure for manipulating intervals on sequences")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides efficient low-level and highly reusable S4 classes
|
|
|
|
|
for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
|
|
|
|
|
generally, data that can be organized sequentially (formally defined as
|
|
|
|
|
@code{Vector} objects), as well as views on these @code{Vector} objects.
|
|
|
|
|
Efficient list-like classes are also provided for storing big collections of
|
|
|
|
|
instances of the basic classes. All classes in the package use consistent
|
|
|
|
|
naming and share the same rich and consistent \"Vector API\" as much as
|
|
|
|
|
possible.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 11:07:56 +00:00
|
|
|
|
(define-public r-genomeinfodb
|
|
|
|
|
(package
|
|
|
|
|
(name "r-genomeinfodb")
|
2016-05-10 09:47:44 +00:00
|
|
|
|
(version "1.8.0")
|
2015-12-18 11:07:56 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "GenomeInfoDb" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:47:44 +00:00
|
|
|
|
"0fcfzw3d0rxlc320bvz0vlxg26fa1278abhjmknb815046g7fn3s"))))
|
2015-12-18 11:07:56 +00:00
|
|
|
|
(properties
|
2016-01-07 15:44:47 +00:00
|
|
|
|
`((upstream-name . "GenomeInfoDb")))
|
2015-12-18 11:07:56 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/GenomeInfoDb")
|
|
|
|
|
(synopsis "Utilities for manipulating chromosome identifiers")
|
|
|
|
|
(description
|
|
|
|
|
"This package contains data and functions that define and allow
|
|
|
|
|
translation between different chromosome sequence naming conventions (e.g.,
|
|
|
|
|
\"chr1\" versus \"1\"), including a function that attempts to place sequence
|
|
|
|
|
names in their natural, rather than lexicographic, order.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-30 13:03:56 +00:00
|
|
|
|
(define-public r-variantannotation
|
|
|
|
|
(package
|
|
|
|
|
(name "r-variantannotation")
|
2016-05-10 09:48:30 +00:00
|
|
|
|
(version "1.18.0")
|
2016-03-30 13:03:56 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "VariantAnnotation" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:48:30 +00:00
|
|
|
|
"1mjm5kav0mjymcj3ha1jnw9snym39w5vc2zkl25dpg78nl00nwar"))))
|
2016-03-30 13:03:56 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "VariantAnnotation")))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)
|
|
|
|
|
("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-bsgenome" ,r-bsgenome)
|
|
|
|
|
("r-dbi" ,r-dbi)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicfeatures" ,r-genomicfeatures)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-summarizedexperiment" ,r-summarizedexperiment)
|
|
|
|
|
("r-rsamtools" ,r-rsamtools)
|
|
|
|
|
("r-zlibbioc" ,r-zlibbioc)))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(home-page "https://bioconductor.org/packages/VariantAnnotation")
|
|
|
|
|
(synopsis "Package for annotation of genetic variants")
|
|
|
|
|
(description "This R package can annotate variants, compute amino acid
|
|
|
|
|
coding changes and predict coding outcomes.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 11:08:22 +00:00
|
|
|
|
(define-public r-xvector
|
|
|
|
|
(package
|
|
|
|
|
(name "r-xvector")
|
2016-05-10 09:49:19 +00:00
|
|
|
|
(version "0.12.0")
|
2015-12-18 11:08:22 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "XVector" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:49:19 +00:00
|
|
|
|
"0c9cqjcxxks3an4wiq167h2grxlfyazajn7bmxhbk42zifp8vmqp"))))
|
2015-12-18 11:08:22 +00:00
|
|
|
|
(properties
|
2016-01-07 15:44:47 +00:00
|
|
|
|
`((upstream-name . "XVector")))
|
2015-12-18 11:08:22 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'use-system-zlib
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "DESCRIPTION"
|
|
|
|
|
(("zlibbioc, ") ""))
|
|
|
|
|
(substitute* "NAMESPACE"
|
|
|
|
|
(("import\\(zlibbioc\\)") ""))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/XVector")
|
|
|
|
|
(synopsis "Representation and manpulation of external sequences")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides memory efficient S4 classes for storing sequences
|
|
|
|
|
\"externally\" (behind an R external pointer, or on disk).")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 11:08:41 +00:00
|
|
|
|
(define-public r-genomicranges
|
|
|
|
|
(package
|
|
|
|
|
(name "r-genomicranges")
|
2016-05-10 09:49:57 +00:00
|
|
|
|
(version "1.24.0")
|
2015-12-18 11:08:41 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "GenomicRanges" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:49:57 +00:00
|
|
|
|
"1iyzg1npl3rnnslwq3h759vf0xhshnn5v801rnlj6bnxzhn9yaqh"))))
|
2015-12-18 11:08:41 +00:00
|
|
|
|
(properties
|
2016-01-07 15:44:47 +00:00
|
|
|
|
`((upstream-name . "GenomicRanges")))
|
2015-12-18 11:08:41 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/GenomicRanges")
|
|
|
|
|
(synopsis "Representation and manipulation of genomic intervals")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides tools to efficiently represent and manipulate
|
|
|
|
|
genomic annotations and alignments is playing a central role when it comes to
|
|
|
|
|
analyzing high-throughput sequencing data (a.k.a. NGS data). The
|
|
|
|
|
GenomicRanges package defines general purpose containers for storing and
|
|
|
|
|
manipulating genomic intervals and variables defined along a genome.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:06:09 +00:00
|
|
|
|
(define-public r-biobase
|
|
|
|
|
(package
|
|
|
|
|
(name "r-biobase")
|
2016-05-10 09:50:35 +00:00
|
|
|
|
(version "2.32.0")
|
2015-12-18 13:06:09 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "Biobase" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:50:35 +00:00
|
|
|
|
"0q4icv9n5rc2qfkv6k1wjhmfcpzcyr8f45m2z3xharbdv912kl1i"))))
|
2015-12-18 13:06:09 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "Biobase")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/Biobase")
|
|
|
|
|
(synopsis "Base functions for Bioconductor")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides functions that are needed by many other packages
|
|
|
|
|
on Bioconductor or which replace R functions.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:06:28 +00:00
|
|
|
|
(define-public r-annotationdbi
|
|
|
|
|
(package
|
|
|
|
|
(name "r-annotationdbi")
|
2016-05-10 09:51:18 +00:00
|
|
|
|
(version "1.34.0")
|
2015-12-18 13:06:28 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "AnnotationDbi" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:51:18 +00:00
|
|
|
|
"0ri766402q3r4fdgibhb7ij7r73g6gdsj1g6iimm4mcinipfixwj"))))
|
2015-12-18 13:06:28 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "AnnotationDbi")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biobase" ,r-biobase)
|
|
|
|
|
("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-dbi" ,r-dbi)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-rsqlite" ,r-rsqlite)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/AnnotationDbi")
|
|
|
|
|
(synopsis "Annotation database interface")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides user interface and database connection code for
|
|
|
|
|
annotation data packages using SQLite data storage.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:06:52 +00:00
|
|
|
|
(define-public r-biomart
|
|
|
|
|
(package
|
|
|
|
|
(name "r-biomart")
|
2016-05-10 09:51:53 +00:00
|
|
|
|
(version "2.28.0")
|
2015-12-18 13:06:52 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "biomaRt" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:51:53 +00:00
|
|
|
|
"1g0w6an9hkflgyhvq6pmrs92s93qarv23v636b9a4bz771wjvm5v"))))
|
2015-12-18 13:06:52 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "biomaRt")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)
|
|
|
|
|
("r-rcurl" ,r-rcurl)
|
|
|
|
|
("r-xml" ,r-xml)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/biomaRt")
|
|
|
|
|
(synopsis "Interface to BioMart databases")
|
|
|
|
|
(description
|
|
|
|
|
"biomaRt provides an interface to a growing collection of databases
|
|
|
|
|
implementing the @url{BioMart software suite, http://www.biomart.org}. The
|
|
|
|
|
package enables retrieval of large amounts of data in a uniform way without
|
|
|
|
|
the need to know the underlying database schemas or write complex SQL queries.
|
|
|
|
|
Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
|
|
|
|
|
Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
|
|
|
|
|
users direct access to a diverse set of data and enable a wide range of
|
|
|
|
|
powerful online queries from gene annotation to database mining.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:07:08 +00:00
|
|
|
|
(define-public r-biocparallel
|
|
|
|
|
(package
|
|
|
|
|
(name "r-biocparallel")
|
2016-05-10 09:52:32 +00:00
|
|
|
|
(version "1.6.0")
|
2015-12-18 13:07:08 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "BiocParallel" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:52:32 +00:00
|
|
|
|
"0yhjihbggs3mn4z43s3fsf70brzjvbilm9ljz1z326xwmk7j40ys"))))
|
2015-12-18 13:07:08 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "BiocParallel")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-futile-logger" ,r-futile-logger)
|
|
|
|
|
("r-snow" ,r-snow)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/BiocParallel")
|
|
|
|
|
(synopsis "Bioconductor facilities for parallel evaluation")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides modified versions and novel implementation of
|
|
|
|
|
functions for parallel evaluation, tailored to use with Bioconductor
|
|
|
|
|
objects.")
|
|
|
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
|
|
2015-12-18 13:07:32 +00:00
|
|
|
|
(define-public r-biostrings
|
|
|
|
|
(package
|
|
|
|
|
(name "r-biostrings")
|
2016-05-10 09:53:48 +00:00
|
|
|
|
(version "2.40.0")
|
2015-12-18 13:07:32 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "Biostrings" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:53:48 +00:00
|
|
|
|
"03gyhiz14xy51nzg0glihk1rv19pq4p1aa3y5g23bzcshs67ggj9"))))
|
2015-12-18 13:07:32 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "Biostrings")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/Biostrings")
|
|
|
|
|
(synopsis "String objects and algorithms for biological sequences")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides memory efficient string containers, string
|
|
|
|
|
matching algorithms, and other utilities, for fast manipulation of large
|
|
|
|
|
biological sequences or sets of sequences.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:07:56 +00:00
|
|
|
|
(define-public r-rsamtools
|
|
|
|
|
(package
|
|
|
|
|
(name "r-rsamtools")
|
2016-05-10 09:54:43 +00:00
|
|
|
|
(version "1.24.0")
|
2015-12-18 13:07:56 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "Rsamtools" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:54:43 +00:00
|
|
|
|
"0w0drs8cpk8nlazq64ag7nm1w5jd1m8riialivm01hz5zcra7scb"))))
|
2015-12-18 13:07:56 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "Rsamtools")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'use-system-zlib
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "DESCRIPTION"
|
|
|
|
|
(("zlibbioc, ") ""))
|
|
|
|
|
(substitute* "NAMESPACE"
|
|
|
|
|
(("import\\(zlibbioc\\)") ""))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-biocparallel" ,r-biocparallel)
|
|
|
|
|
("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-bitops" ,r-bitops)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
|
|
|
|
|
(synopsis "Interface to samtools, bcftools, and tabix")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides an interface to the 'samtools', 'bcftools', and
|
|
|
|
|
'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
|
|
|
|
|
binary variant call (BCF) and compressed indexed tab-delimited (tabix)
|
|
|
|
|
files.")
|
|
|
|
|
(license license:expat)))
|
|
|
|
|
|
2015-12-18 13:08:17 +00:00
|
|
|
|
(define-public r-summarizedexperiment
|
|
|
|
|
(package
|
|
|
|
|
(name "r-summarizedexperiment")
|
2016-05-10 09:57:39 +00:00
|
|
|
|
(version "1.2.0")
|
2015-12-18 13:08:17 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "SummarizedExperiment" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:57:39 +00:00
|
|
|
|
"1pfbw2dlifa7m7gxpazb6z517kw3p5a3khslykcy7gml5xsf2ch8"))))
|
2015-12-18 13:08:17 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "SummarizedExperiment")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biobase" ,r-biobase)
|
|
|
|
|
("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/SummarizedExperiment")
|
|
|
|
|
(synopsis "Container for representing genomic ranges by sample")
|
|
|
|
|
(description
|
|
|
|
|
"The SummarizedExperiment container contains one or more assays, each
|
|
|
|
|
represented by a matrix-like object of numeric or other mode. The rows
|
|
|
|
|
typically represent genomic ranges of interest and the columns represent
|
|
|
|
|
samples.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:08:36 +00:00
|
|
|
|
(define-public r-genomicalignments
|
|
|
|
|
(package
|
|
|
|
|
(name "r-genomicalignments")
|
2016-05-10 09:59:33 +00:00
|
|
|
|
(version "1.8.0")
|
2015-12-18 13:08:36 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "GenomicAlignments" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 09:59:33 +00:00
|
|
|
|
"1y4qgqxq8dax9swgl59m6i7ggjpqrjllgx87b9vwls3z0nf1i6xj"))))
|
2015-12-18 13:08:36 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "GenomicAlignments")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-biocparallel" ,r-biocparallel)
|
|
|
|
|
("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-rsamtools" ,r-rsamtools)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)
|
|
|
|
|
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/GenomicAlignments")
|
|
|
|
|
(synopsis "Representation and manipulation of short genomic alignments")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides efficient containers for storing and manipulating
|
|
|
|
|
short genomic alignments (typically obtained by aligning short reads to a
|
|
|
|
|
reference genome). This includes read counting, computing the coverage,
|
|
|
|
|
junction detection, and working with the nucleotide content of the
|
|
|
|
|
alignments.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:09:00 +00:00
|
|
|
|
(define-public r-rtracklayer
|
|
|
|
|
(package
|
|
|
|
|
(name "r-rtracklayer")
|
2016-05-10 10:00:12 +00:00
|
|
|
|
(version "1.32.0")
|
2015-12-18 13:09:00 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "rtracklayer" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:00:12 +00:00
|
|
|
|
"0nrwk1g8b1ymvbgnqniimbvwfq13r01va9rx3b03xj4hpywzy5nv"))))
|
2015-12-18 13:09:00 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'use-system-zlib
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "DESCRIPTION"
|
|
|
|
|
(("zlibbioc, ") ""))
|
|
|
|
|
(substitute* "NAMESPACE"
|
|
|
|
|
(("import\\(zlibbioc\\)") ""))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicalignments" ,r-genomicalignments)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-rcurl" ,r-rcurl)
|
|
|
|
|
("r-rsamtools" ,r-rsamtools)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)
|
|
|
|
|
("r-xml" ,r-xml)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/rtracklayer")
|
|
|
|
|
(synopsis "R interface to genome browsers and their annotation tracks")
|
|
|
|
|
(description
|
|
|
|
|
"rtracklayer is an extensible framework for interacting with multiple
|
|
|
|
|
genome browsers (currently UCSC built-in) and manipulating annotation tracks
|
|
|
|
|
in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
|
|
|
|
|
built-in). The user may export/import tracks to/from the supported browsers,
|
|
|
|
|
as well as query and modify the browser state, such as the current viewport.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-18 13:09:18 +00:00
|
|
|
|
(define-public r-genomicfeatures
|
|
|
|
|
(package
|
|
|
|
|
(name "r-genomicfeatures")
|
2016-05-10 10:00:42 +00:00
|
|
|
|
(version "1.24.0")
|
2015-12-18 13:09:18 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "GenomicFeatures" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:00:42 +00:00
|
|
|
|
"1rfqxq6brrfzdajxd6ydbfaag0529d1cpjihvagmf8124prx2b2f"))))
|
2015-12-18 13:09:18 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "GenomicFeatures")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)
|
|
|
|
|
("r-biobase" ,r-biobase)
|
|
|
|
|
("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-biomart" ,r-biomart)
|
|
|
|
|
("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-dbi" ,r-dbi)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-rcurl" ,r-rcurl)
|
|
|
|
|
("r-rsqlite" ,r-rsqlite)
|
|
|
|
|
("r-rtracklayer" ,r-rtracklayer)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/GenomicFeatures")
|
|
|
|
|
(synopsis "Tools for working with transcript centric annotations")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides a set of tools and methods for making and
|
|
|
|
|
manipulating transcript centric annotations. With these tools the user can
|
|
|
|
|
easily download the genomic locations of the transcripts, exons and cds of a
|
|
|
|
|
given organism, from either the UCSC Genome Browser or a BioMart
|
|
|
|
|
database (more sources will be supported in the future). This information is
|
|
|
|
|
then stored in a local database that keeps track of the relationship between
|
|
|
|
|
transcripts, exons, cds and genes. Flexible methods are provided for
|
|
|
|
|
extracting the desired features in a convenient format.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-23 16:25:59 +00:00
|
|
|
|
(define-public r-go-db
|
|
|
|
|
(package
|
|
|
|
|
(name "r-go-db")
|
|
|
|
|
(version "3.2.2")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-02-29 08:46:58 +00:00
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/GO.db_"
|
|
|
|
|
version ".tar.gz"))
|
2015-12-23 16:25:59 +00:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"00gariag9ampz82dh0xllrc26r85d7vdcwc0vca5zdy147rwxr7f"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "GO.db")))
|
|
|
|
|
(build-system r-build-system)
|
2016-01-13 15:24:44 +00:00
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)))
|
2015-12-23 16:25:59 +00:00
|
|
|
|
(home-page "http://bioconductor.org/packages/GO.db")
|
|
|
|
|
(synopsis "Annotation maps describing the entire Gene Ontology")
|
|
|
|
|
(description
|
|
|
|
|
"The purpose of this GO.db annotation package is to provide detailed
|
|
|
|
|
information about the latest version of the Gene Ontologies.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-01-13 15:26:13 +00:00
|
|
|
|
(define-public r-graph
|
|
|
|
|
(package
|
|
|
|
|
(name "r-graph")
|
2016-05-10 10:01:09 +00:00
|
|
|
|
(version "1.50.0")
|
2016-01-13 15:26:13 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "graph" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:01:09 +00:00
|
|
|
|
"0ys5s19m5r30rlr0fnx2h0z2qw7n2xrad4l2yfb1bbrk8dwyf4pi"))))
|
2016-01-13 15:26:13 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/graph")
|
|
|
|
|
(synopsis "Handle graph data structures in R")
|
|
|
|
|
(description
|
|
|
|
|
"This package implements some simple graph handling capabilities for R.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-23 16:31:03 +00:00
|
|
|
|
(define-public r-topgo
|
|
|
|
|
(package
|
|
|
|
|
(name "r-topgo")
|
2016-05-10 10:01:42 +00:00
|
|
|
|
(version "2.24.0")
|
2015-12-23 16:31:03 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "topGO" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:01:42 +00:00
|
|
|
|
"1p4vsl32qhjw15yv9ym01ni63gjg73jaghlf17wc4zfn3iaz2zar"))))
|
2015-12-23 16:31:03 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "topGO")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)
|
|
|
|
|
("r-biobase" ,r-biobase)
|
|
|
|
|
("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-go-db" ,r-go-db)
|
2016-05-10 10:01:42 +00:00
|
|
|
|
("r-matrixstats" ,r-matrixstats)
|
2016-01-13 15:26:37 +00:00
|
|
|
|
("r-graph" ,r-graph)
|
2015-12-23 16:31:03 +00:00
|
|
|
|
("r-sparsem" ,r-sparsem)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/topGO")
|
|
|
|
|
(synopsis "Enrichment analysis for gene ontology")
|
|
|
|
|
(description
|
|
|
|
|
"The topGO package provides tools for testing @dfn{gene ontology} (GO)
|
|
|
|
|
terms while accounting for the topology of the GO graph. Different test
|
|
|
|
|
statistics and different methods for eliminating local similarities and
|
|
|
|
|
dependencies between GO terms can be implemented and applied.")
|
|
|
|
|
;; Any version of the LGPL applies.
|
|
|
|
|
(license license:lgpl2.1+)))
|
|
|
|
|
|
2015-12-23 16:34:07 +00:00
|
|
|
|
(define-public r-bsgenome
|
|
|
|
|
(package
|
|
|
|
|
(name "r-bsgenome")
|
2016-05-10 10:02:26 +00:00
|
|
|
|
(version "1.40.0")
|
2015-12-23 16:34:07 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "BSgenome" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:02:26 +00:00
|
|
|
|
"08g3w47ysbmgj4hclb0x2wsn7pi9cnm3xkkfk4shgrka2g23qz44"))))
|
2015-12-23 16:34:07 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "BSgenome")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biocgenerics" ,r-biocgenerics)
|
|
|
|
|
("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-rsamtools" ,r-rsamtools)
|
|
|
|
|
("r-rtracklayer" ,r-rtracklayer)
|
|
|
|
|
("r-s4vectors" ,r-s4vectors)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/BSgenome")
|
|
|
|
|
(synopsis "Infrastructure for Biostrings-based genome data packages")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides infrastructure shared by all Biostrings-based
|
|
|
|
|
genome data packages and support for efficient SNP representation.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-12-23 16:34:27 +00:00
|
|
|
|
(define-public r-impute
|
|
|
|
|
(package
|
|
|
|
|
(name "r-impute")
|
2016-05-10 10:02:48 +00:00
|
|
|
|
(version "1.46.0")
|
2015-12-23 16:34:27 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "impute" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:02:48 +00:00
|
|
|
|
"0v9ibgv8kp8il52miz7b7z65mv6irqxylx6lfzkxgvxd970dgrz0"))))
|
2015-12-23 16:34:27 +00:00
|
|
|
|
(inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(home-page "http://bioconductor.org/packages/impute")
|
|
|
|
|
(synopsis "Imputation for microarray data")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides a function to impute missing gene expression
|
|
|
|
|
microarray data, using nearest neighbor averaging.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2015-12-23 16:34:45 +00:00
|
|
|
|
(define-public r-seqpattern
|
|
|
|
|
(package
|
|
|
|
|
(name "r-seqpattern")
|
2016-05-10 10:03:08 +00:00
|
|
|
|
(version "1.4.0")
|
2015-12-23 16:34:45 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "seqPattern" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:03:08 +00:00
|
|
|
|
"1dj9hfnbdj11yjxwd8jmxrdkj7n6gmaaj6244g2psgarhjcp4wfb"))))
|
2015-12-23 16:34:45 +00:00
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "seqPattern")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-plotrix" ,r-plotrix)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/seqPattern")
|
|
|
|
|
(synopsis "Visualising oligonucleotide patterns and motif occurrences")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides tools to visualize oligonucleotide patterns and
|
|
|
|
|
sequence motif occurrences across a large set of sequences centred at a common
|
|
|
|
|
reference point and sorted by a user defined feature.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2015-12-23 16:35:04 +00:00
|
|
|
|
(define-public r-genomation
|
|
|
|
|
(package
|
|
|
|
|
(name "r-genomation")
|
2016-05-10 10:03:32 +00:00
|
|
|
|
(version "1.4.0")
|
2015-12-23 16:35:04 +00:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "genomation" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:03:32 +00:00
|
|
|
|
"16q1qkl6cwwj5hqhxpfgbz0y27hwz3h8zkjxpbyvjy1q0894sdjl"))))
|
2015-12-23 16:35:04 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-bsgenome" ,r-bsgenome)
|
|
|
|
|
("r-data-table" ,r-data-table)
|
|
|
|
|
("r-genomeinfodb" ,r-genomeinfodb)
|
|
|
|
|
("r-genomicalignments" ,r-genomicalignments)
|
|
|
|
|
("r-genomicranges" ,r-genomicranges)
|
|
|
|
|
("r-ggplot2" ,r-ggplot2)
|
|
|
|
|
("r-gridbase" ,r-gridbase)
|
|
|
|
|
("r-impute" ,r-impute)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-matrixstats" ,r-matrixstats)
|
|
|
|
|
("r-plotrix" ,r-plotrix)
|
|
|
|
|
("r-plyr" ,r-plyr)
|
|
|
|
|
("r-readr" ,r-readr)
|
|
|
|
|
("r-reshape2" ,r-reshape2)
|
|
|
|
|
("r-rsamtools" ,r-rsamtools)
|
|
|
|
|
("r-rtracklayer" ,r-rtracklayer)
|
|
|
|
|
("r-seqpattern" ,r-seqpattern)))
|
|
|
|
|
(home-page "http://bioinformatics.mdc-berlin.de/genomation/")
|
|
|
|
|
(synopsis "Summary, annotation and visualization of genomic data")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides a package for summary and annotation of genomic
|
|
|
|
|
intervals. Users can visualize and quantify genomic intervals over
|
|
|
|
|
pre-defined functional regions, such as promoters, exons, introns, etc. The
|
|
|
|
|
genomic intervals represent regions with a defined chromosome position, which
|
|
|
|
|
may be associated with a score, such as aligned reads from HT-seq experiments,
|
|
|
|
|
TF binding sites, methylation scores, etc. The package can use any tabular
|
|
|
|
|
genomic feature data as long as it has minimal information on the locations of
|
|
|
|
|
genomic intervals. In addition, it can use BAM or BigWig files as input.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-01-13 15:27:29 +00:00
|
|
|
|
(define-public r-org-hs-eg-db
|
|
|
|
|
(package
|
|
|
|
|
(name "r-org-hs-eg-db")
|
|
|
|
|
(version "3.2.3")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"org.Hs.eg.db_" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0xicgkbh6xkvs74s1piafqac63dyz2ycdyil4pj4ghhxx2sabm6p"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "org.Hs.eg.db")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)))
|
|
|
|
|
(home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/")
|
|
|
|
|
(synopsis "Genome wide annotation for Human")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides mappings from Entrez gene identifiers to various
|
|
|
|
|
annotations for the human genome.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-02-16 16:19:30 +00:00
|
|
|
|
(define-public r-org-ce-eg-db
|
|
|
|
|
(package
|
|
|
|
|
(name "r-org-ce-eg-db")
|
|
|
|
|
(version "3.2.3")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"org.Ce.eg.db_" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1d0lx00ybq34yqs6mziaa0lrh77xm0ggsmi76g6k95f77gi7m1sw"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "org.Ce.eg.db")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)))
|
|
|
|
|
(home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/")
|
|
|
|
|
(synopsis "Genome wide annotation for Worm")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides mappings from Entrez gene identifiers to various
|
|
|
|
|
annotations for the genome of the model worm Caenorhabditis elegans.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-02-16 16:19:55 +00:00
|
|
|
|
(define-public r-org-dm-eg-db
|
|
|
|
|
(package
|
|
|
|
|
(name "r-org-dm-eg-db")
|
|
|
|
|
(version "3.2.3")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"org.Dm.eg.db_" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0mib46c7nr00l7mh290n383za9hyl91a1dc6jhjbk884jmxaxyz6"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "org.Dm.eg.db")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)))
|
|
|
|
|
(home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/")
|
|
|
|
|
(synopsis "Genome wide annotation for Fly")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides mappings from Entrez gene identifiers to various
|
|
|
|
|
annotations for the genome of the model fruit fly Drosophila melanogaster.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-02-16 16:20:32 +00:00
|
|
|
|
(define-public r-org-mm-eg-db
|
|
|
|
|
(package
|
|
|
|
|
(name "r-org-mm-eg-db")
|
|
|
|
|
(version "3.2.3")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"org.Mm.eg.db_" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0wh1pm3npdg7070875kfgiid3bqkz3q7rq6snhk6bxfvph00298y"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "org.Mm.eg.db")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-annotationdbi" ,r-annotationdbi)))
|
|
|
|
|
(home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/")
|
|
|
|
|
(synopsis "Genome wide annotation for Mouse")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides mappings from Entrez gene identifiers to various
|
|
|
|
|
annotations for the genome of the model mouse Mus musculus.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-18 11:15:24 +00:00
|
|
|
|
(define-public r-seqlogo
|
|
|
|
|
(package
|
|
|
|
|
(name "r-seqlogo")
|
2016-05-10 10:03:58 +00:00
|
|
|
|
(version "1.38.0")
|
2016-03-18 11:15:24 +00:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "seqLogo" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-05-10 10:03:58 +00:00
|
|
|
|
"01jddx62nhi3r7czbh9hxy0wwpazbc9ax1fgagfxl6p4kx9xz9rb"))))
|
2016-03-18 11:15:24 +00:00
|
|
|
|
(properties `((upstream-name . "seqLogo")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(home-page "http://bioconductor.org/packages/seqLogo")
|
|
|
|
|
(synopsis "Sequence logos for DNA sequence alignments")
|
|
|
|
|
(description
|
|
|
|
|
"seqLogo takes the position weight matrix of a DNA sequence motif and
|
|
|
|
|
plots the corresponding sequence logo as introduced by Schneider and
|
|
|
|
|
Stephens (1990).")
|
|
|
|
|
(license license:lgpl2.0+)))
|
|
|
|
|
|
2016-03-18 11:15:50 +00:00
|
|
|
|
(define-public r-bsgenome-hsapiens-ucsc-hg19
|
|
|
|
|
(package
|
|
|
|
|
(name "r-bsgenome-hsapiens-ucsc-hg19")
|
|
|
|
|
(version "1.4.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"BSgenome.Hsapiens.UCSC.hg19_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
;; As this package provides little more than a very large data file it
|
|
|
|
|
;; doesn't make sense to build substitutes.
|
|
|
|
|
(arguments `(#:substitutable? #f))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-bsgenome" ,r-bsgenome)))
|
|
|
|
|
(home-page
|
|
|
|
|
"http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
|
|
|
|
|
(synopsis "Full genome sequences for Homo sapiens")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides full genome sequences for Homo sapiens as provided
|
|
|
|
|
by UCSC (hg19, February 2009) and stored in Biostrings objects.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-30 10:23:51 +00:00
|
|
|
|
(define-public r-bsgenome-mmusculus-ucsc-mm9
|
|
|
|
|
(package
|
|
|
|
|
(name "r-bsgenome-mmusculus-ucsc-mm9")
|
|
|
|
|
(version "1.4.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"BSgenome.Mmusculus.UCSC.mm9_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
;; As this package provides little more than a very large data file it
|
|
|
|
|
;; doesn't make sense to build substitutes.
|
|
|
|
|
(arguments `(#:substitutable? #f))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-bsgenome" ,r-bsgenome)))
|
|
|
|
|
(home-page
|
|
|
|
|
"http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
|
|
|
|
|
(synopsis "Full genome sequences for Mouse")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides full genome sequences for Mus musculus (Mouse) as
|
|
|
|
|
provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-30 10:24:16 +00:00
|
|
|
|
(define-public r-bsgenome-celegans-ucsc-ce6
|
|
|
|
|
(package
|
|
|
|
|
(name "r-bsgenome-celegans-ucsc-ce6")
|
|
|
|
|
(version "1.4.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"BSgenome.Celegans.UCSC.ce6_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
;; As this package provides little more than a very large data file it
|
|
|
|
|
;; doesn't make sense to build substitutes.
|
|
|
|
|
(arguments `(#:substitutable? #f))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-bsgenome" ,r-bsgenome)))
|
|
|
|
|
(home-page
|
|
|
|
|
"http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
|
|
|
|
|
(synopsis "Full genome sequences for Worm")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides full genome sequences for Caenorhabditis
|
|
|
|
|
elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
|
|
|
|
|
objects.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-30 10:24:44 +00:00
|
|
|
|
(define-public r-bsgenome-dmelanogaster-ucsc-dm3
|
|
|
|
|
(package
|
|
|
|
|
(name "r-bsgenome-dmelanogaster-ucsc-dm3")
|
|
|
|
|
(version "1.4.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; We cannot use bioconductor-uri here because this tarball is
|
|
|
|
|
;; located under "data/annotation/" instead of "bioc/".
|
|
|
|
|
(uri (string-append "http://www.bioconductor.org/packages/"
|
|
|
|
|
"release/data/annotation/src/contrib/"
|
|
|
|
|
"BSgenome.Dmelanogaster.UCSC.dm3_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
;; As this package provides little more than a very large data file it
|
|
|
|
|
;; doesn't make sense to build substitutes.
|
|
|
|
|
(arguments `(#:substitutable? #f))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-bsgenome" ,r-bsgenome)))
|
|
|
|
|
(home-page
|
|
|
|
|
"http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
|
|
|
|
|
(synopsis "Full genome sequences for Fly")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides full genome sequences for Drosophila
|
|
|
|
|
melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
|
|
|
|
|
Biostrings objects.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2016-03-18 11:16:17 +00:00
|
|
|
|
(define-public r-motifrg
|
|
|
|
|
(package
|
|
|
|
|
(name "r-motifrg")
|
|
|
|
|
(version "1.14.0")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "motifRG" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn"))))
|
|
|
|
|
(properties `((upstream-name . "motifRG")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-biostrings" ,r-biostrings)
|
|
|
|
|
("r-bsgenome" ,r-bsgenome)
|
|
|
|
|
("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
|
|
|
|
|
("r-iranges" ,r-iranges)
|
|
|
|
|
("r-seqlogo" ,r-seqlogo)
|
|
|
|
|
("r-xvector" ,r-xvector)))
|
|
|
|
|
(home-page "http://bioconductor.org/packages/motifRG")
|
|
|
|
|
(synopsis "Discover motifs in high throughput sequencing data")
|
|
|
|
|
(description
|
|
|
|
|
"This package provides tools for discriminative motif discovery in high
|
|
|
|
|
throughput genetic sequencing data sets using regression methods.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-09-19 22:32:45 +00:00
|
|
|
|
(define-public r-qtl
|
|
|
|
|
(package
|
|
|
|
|
(name "r-qtl")
|
2016-04-19 15:45:55 +00:00
|
|
|
|
(version "1.39-5")
|
2015-09-19 22:32:45 +00:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://cran/src/contrib/qtl_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-04-19 15:45:55 +00:00
|
|
|
|
"1grwgvyv7x0dgay1858bg7qf4wk47gpnq7qkqpcda9cn0h970d6f"))))
|
2015-09-19 22:32:45 +00:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(home-page "http://rqtl.org/")
|
|
|
|
|
(synopsis "R package for analyzing QTL experiments in genetics")
|
|
|
|
|
(description "R/qtl is an extension library for the R statistics
|
|
|
|
|
system. It is used to analyze experimental crosses for identifying
|
|
|
|
|
genes contributing to variation in quantitative traits (so-called
|
|
|
|
|
quantitative trait loci, QTLs).
|
|
|
|
|
|
|
|
|
|
Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
|
|
|
|
|
identify genotyping errors, and to perform single-QTL and two-QTL,
|
|
|
|
|
two-dimensional genome scans.")
|
|
|
|
|
(license license:gpl3)))
|
2015-10-02 14:37:03 +00:00
|
|
|
|
|
2016-03-30 13:05:31 +00:00
|
|
|
|
(define-public r-zlibbioc
|
|
|
|
|
(package
|
|
|
|
|
(name "r-zlibbioc")
|
|
|
|
|
(version "1.16.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (bioconductor-uri "zlibbioc" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"01wc26ndg4jsn1wyrl6zzq636gxaip5fci0xapym4lh9wryc4wnw"))))
|
|
|
|
|
(properties
|
|
|
|
|
`((upstream-name . "zlibbioc")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(home-page "https://bioconductor.org/packages/zlibbioc")
|
|
|
|
|
(synopsis "Provider for zlib-1.2.5 to R packages")
|
|
|
|
|
(description "This package uses the source code of zlib-1.2.5 to create
|
|
|
|
|
libraries for systems that do not have these available via other means.")
|
|
|
|
|
(license license:artistic2.0)))
|
|
|
|
|
|
2015-10-02 14:37:03 +00:00
|
|
|
|
(define-public pepr
|
|
|
|
|
(package
|
|
|
|
|
(name "pepr")
|
|
|
|
|
(version "1.0.9")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://pypi.python.org/packages/source/P"
|
|
|
|
|
"/PePr/PePr-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:python ,python-2 ; python2 only
|
|
|
|
|
#:tests? #f ; no tests included
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
;; When setuptools is used a ".egg" archive is generated and
|
|
|
|
|
;; installed. This makes it hard to actually run PePr. This issue
|
|
|
|
|
;; has been reported upstream:
|
|
|
|
|
;; https://github.com/shawnzhangyx/PePr/issues/9
|
|
|
|
|
(add-after 'unpack 'disable-egg-generation
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "setup.py"
|
|
|
|
|
(("from setuptools import setup")
|
|
|
|
|
"from distutils.core import setup"))
|
|
|
|
|
#t)))))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("python2-numpy" ,python2-numpy)
|
|
|
|
|
("python2-scipy" ,python2-scipy)
|
|
|
|
|
("python2-pysam" ,python2-pysam)))
|
|
|
|
|
(home-page "https://code.google.com/p/pepr-chip-seq/")
|
|
|
|
|
(synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
|
|
|
|
|
(description
|
|
|
|
|
"PePr is a ChIP-Seq peak calling or differential binding analysis tool
|
|
|
|
|
that is primarily designed for data with biological replicates. It uses a
|
|
|
|
|
negative binomial distribution to model the read counts among the samples in
|
|
|
|
|
the same group, and look for consistent differences between ChIP and control
|
|
|
|
|
group or two ChIP groups run under different conditions.")
|
|
|
|
|
(license license:gpl3+)))
|
2016-04-25 09:17:21 +00:00
|
|
|
|
|
|
|
|
|
(define-public filevercmp
|
|
|
|
|
(let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
|
|
|
|
|
(package
|
|
|
|
|
(name "filevercmp")
|
|
|
|
|
(version (string-append "0-1." (string-take commit 7)))
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/ekg/filevercmp/archive/"
|
|
|
|
|
commit ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; There are no tests to run.
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure) ; There is no configure phase.
|
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
|
|
|
|
(install-file "filevercmp" bin)))))))
|
|
|
|
|
(home-page "https://github.com/ekg/filevercmp")
|
|
|
|
|
(synopsis "This program compares version strings")
|
|
|
|
|
(description "This program compares version strings. It intends to be a
|
|
|
|
|
replacement for strverscmp.")
|
|
|
|
|
(license license:gpl3+))))
|