* [PATCH] gnu: Add subread.
@ 2015-04-16 9:20 Ricardo Wurmus
2015-04-21 8:27 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-04-16 9:20 UTC (permalink / raw)
To: Guix-devel
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From fd34c03a72d280bc623af5edfc2a28a570c26784 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 16 Apr 2015 11:19:45 +0200
Subject: [PATCH] gnu: Add subread.
* gnu/packages/bioinformatics.scm (subread): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0fd6c0c..7da6c75 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1444,6 +1444,45 @@ sequences.")
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+)))
+(define-public subread
+ (package
+ (name "subread")
+ (version "1.4.6-p2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/subread/subread-"
+ version "-source.tar.gz"))
+ (sha256
+ (base32
+ "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:make-flags '("-f" "Makefile.Linux")
+ #:phases
+ (alist-cons-after
+ 'unpack 'enter-dir
+ (lambda _ (chdir "src") #t)
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin)))
+ ;; no "configure" script
+ (alist-delete 'configure %standard-phases)))))
+ (inputs `(("zlib" ,zlib)))
+ (home-page "http://bioinf.wehi.edu.au/subread-package/")
+ (synopsis "Tool kit for processing next-gen sequencing data")
+ (description
+ "The subread package contains the following tools: subread aligner, a
+general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
+and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
+features; exactSNP: a SNP caller that discovers SNPs by testing signals
+against local background noises.")
+ (license license:gpl3+)))
+
(define-public shogun
(package
(name "shogun")
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] gnu: Add subread.
2015-04-16 9:20 [PATCH] gnu: Add subread Ricardo Wurmus
@ 2015-04-21 8:27 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-04-21 8:27 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From fd34c03a72d280bc623af5edfc2a28a570c26784 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 16 Apr 2015 11:19:45 +0200
> Subject: [PATCH] gnu: Add subread.
>
> * gnu/packages/bioinformatics.scm (subread): New variable.
LGTM!
Ludo'.
^ permalink raw reply [flat|nested] 2+ messages in thread
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