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02/02: gnu: Add samtools
From: |
Ludovic Courtès |
Subject: |
02/02: gnu: Add samtools |
Date: |
Fri, 12 Dec 2014 23:01:13 +0000 |
civodul pushed a commit to branch master
in repository guix.
commit 4e10a22168248bbbb78cd8603bb9b8a3a26b90c7
Author: Ricardo Wurmus <address@hidden>
Date: Thu Dec 11 15:48:22 2014 +0100
gnu: Add samtools
* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
Signed-off-by: Ludovic Courtès <address@hidden>
---
gnu-system.am | 1 +
gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++
2 files changed, 85 insertions(+), 0 deletions(-)
diff --git a/gnu-system.am b/gnu-system.am
index 2854fb5..e828c01 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 0000000..6f6178a
--- /dev/null
+++ b/gnu/packages/bioinformatics.scm
@@ -0,0 +1,84 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014 Ricardo Wurmus <address@hidden>
+;;;
+;;; 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)))