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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-06-01 15:06:04 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-06-02 14:30:14 +0200
commite7c097306dea32cece9b2001ffc9918e1076677f (patch)
treec2351fc7e890d6ad53f5b4d9b72f88bccb5c3a7f /gnu
parent132b4c8c235e599a28604facce7ecee01b4a446e (diff)
gnu: Add HTSlib.
* gnu/packages/bioinformatics.scm (htslib): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm35
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f66ea26b2a..c7836f173e 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 macs
(package
(name "macs")