From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Add MOSAIK.
Date: Fri, 16 Oct 2015 17:43:09 +0200 [thread overview]
Message-ID: <idjziziyg36.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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From 2f5755ddad550cf811f97ad6889eea2a7171a1c3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 16 Oct 2015 17:41:07 +0200
Subject: [PATCH] gnu: Add MOSAIK.
* gnu/packages/bioinformatics.scm (mosaik): New variable.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 069e52f..e339a70 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2248,6 +2248,52 @@ viewer.")
(string-append bin "/samtools")))))
(delete 'patch-tests)))))))
+(define-public mosaik
+ (let ((commit "5c25216d"))
+ (package
+ (name "mosaik")
+ (version "2.2.30")
+ (source (origin
+ ;; There are no release tarballs nor tags.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wanpinglee/MOSAIK.git")
+ (commit commit)))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32
+ "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:make-flags (list "CC=gcc")
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda _ (chdir "src") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin)
+ #t))))))
+ (inputs
+ `(("perl" ,perl)
+ ("zlib" ,zlib)))
+ (home-page "https://code.google.com/p/mosaik-aligner/")
+ (synopsis "Map nucleotide sequence reads to reference genomes")
+ (description
+ "MOSAIK is a program for mapping second and third-generation sequencing
+reads to a reference genome. MOSAIK can align reads generated by all the
+major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
+Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
+ ;; MOSAIK is released under the GPLv2+ with the exception of third-party
+ ;; code released into the public domain:
+ ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
+ ;; 2. MD5 implementation - RSA Data Security, RFC 1321
+ (license (list license:gpl2+ license:public-domain)))))
+
(define-public ngs-sdk
(package
(name "ngs-sdk")
--
2.1.0
next reply other threads:[~2015-10-16 15:43 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-10-16 15:43 Ricardo Wurmus [this message]
2015-10-19 15:51 ` [PATCH] Add MOSAIK Ludovic Courtès
2015-10-23 8:02 ` Andreas Enge
2015-10-23 8:42 ` Ricardo Wurmus
2015-10-27 11:42 ` Efraim Flashner
2015-10-27 12:51 ` Ricardo Wurmus
2015-10-27 15:50 ` Ludovic Courtès
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