diff options
| -rw-r--r-- | gnu-system.am | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 84 |
2 files changed, 85 insertions, 0 deletions
diff --git a/gnu-system.am b/gnu-system.am index 2854fb511d..e828c01d7c 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -45,6 +45,7 @@ GNU_SYSTEM_MODULES = \ gnu/packages/base.scm \ gnu/packages/bash.scm \ gnu/packages/bdw-gc.scm \ + gnu/packages/bioinformatics.scm \ gnu/packages/bittorrent.scm \ gnu/packages/bison.scm \ gnu/packages/boost.scm \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm new file mode 100644 index 0000000000..6f6178a3ff --- /dev/null +++ b/gnu/packages/bioinformatics.scm @@ -0,0 +1,84 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net> +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. + +(define-module (gnu packages bioinformatics) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system gnu) + #:use-module (gnu packages) + #:use-module (gnu packages compression) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python)) + +(define-public samtools + (package + (name "samtools") + (version "1.1") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/samtools/" + version "/samtools-" version ".tar.bz2")) + (sha256 + (base32 + "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (alist-cons-after + 'unpack + 'patch-makefile-curses + (lambda _ + (substitute* "Makefile" + (("-lcurses") "-lncurses"))) + (alist-cons-after + 'unpack + 'patch-tests + (lambda* (#:key inputs #:allow-other-keys) + (let ((bash (assoc-ref inputs "bash"))) + (substitute* "test/test.pl" + ;; The test script calls out to /bin/bash + (("/bin/bash") + (string-append bash "/bin/bash")) + ;; There are two failing tests upstream relating to the "stats" + ;; subcommand in test_usage_subcommand ("did not have Usage" + ;; and "usage did not mention samtools stats"), so we disable + ;; them. + (("(test_usage_subcommand\\(.*\\);)" cmd) + (string-append "unless ($subcommand eq 'stats') {" cmd "};"))))) + (alist-delete + 'configure + %standard-phases))))) + (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))) |