From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: "Ludovic Courtès" <ludo@gnu.org>
Cc: guix-devel@gnu.org
Subject: Re: [PATCH] gnu: Add samtools
Date: Fri, 12 Dec 2014 10:48:57 +0100 [thread overview]
Message-ID: <idj4mt1kxkm.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <878uie6pd9.fsf@gnu.org>
[-- Attachment #1: Type: text/plain, Size: 768 bytes --]
Attached is an updated patch.
>> + (synopsis "Efficient utilities on manipulating alignments in the SAM format")
>
> What about “Utilities to manipulate nucleotide sequence alignments”, to
> make it clearer that it’s bioinfo-related?
I chose to reword it as "Utilities to efficiently manipulate nucleotide
sequence alignments"; is this okay?
>> + (description
>> + "Samtools implements various utilities for post-processing alignments in
>> +the SAM, BAM, and CRAM formats, including indexing, variant calling (in
>> +conjunction with bcftools), and a simple alignment viewer.")
>
> Likewise, maybe replace “alignments” with “nucleotide sequence
> alignments” or something to that effect?
I agree. See attached patch.
[-- Attachment #2: 0001-gnu-Add-samtools.patch --]
[-- Type: text/x-patch, Size: 4587 bytes --]
From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 11 Dec 2014 15:48:22 +0100
Subject: [PATCH] gnu: Add samtools
* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
---
gnu-system.am | 1 +
gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 85 insertions(+)
create mode 100644 gnu/packages/bioinformatics.scm
diff --git a/gnu-system.am b/gnu-system.am
index e923340..d4d0b51 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 <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)))
--
1.9.3
next prev parent reply other threads:[~2014-12-12 9:49 UTC|newest]
Thread overview: 11+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-12-11 14:48 [PATCH] gnu: Add samtools Ricardo Wurmus
2014-12-11 17:57 ` Ludovic Courtès
2014-12-12 9:48 ` Ricardo Wurmus [this message]
2014-12-12 22:55 ` Ludovic Courtès
2014-12-13 6:30 ` Mark H Weaver
2014-12-13 8:19 ` Ricardo Wurmus
2014-12-13 15:53 ` Ludovic Courtès
2014-12-13 16:30 ` Mark H Weaver
2014-12-13 17:04 ` Mark H Weaver
2014-12-15 11:36 ` Ricardo Wurmus
2014-12-15 22:12 ` Ludovic Courtès
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