* [PATCH] Add HTSlib.
@ 2015-06-01 13:06 Ricardo Wurmus
2015-06-01 19:41 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-06-01 13:06 UTC (permalink / raw)
To: guix-devel
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From 708093dc001d46a2ec487873e8150861b05872da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 1 Jun 2015 15:06:04 +0200
Subject: [PATCH] gnu: Add HTSlib.
* gnu/packages/bioinformatics.scm (htslib): New variable.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b9a3412..820811d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -919,6 +919,41 @@ sequencing (HTS) data. There are also an number of useful utilities for
manipulating HTS data.")
(license license:expat)))
+(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))))
+
(define-public picard
(package
(name "picard")
--
2.1.0
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