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[PATCH] gnu: Add Ribotaper.
From: |
Ricardo Wurmus |
Subject: |
[PATCH] gnu: Add Ribotaper. |
Date: |
Thu, 7 Jul 2016 11:26:29 +0200 |
* gnu/packages/bioinformatics.scm (bedtools-for-ribotaper, ribotaper):
New variables.
---
gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 294f4ee..c4af842 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -258,6 +258,50 @@ intervals from multiple files in widely-used genomic file
formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:gpl2)))
+;; Later releases of bedtools produce files with more columns than
+;; what Ribotaper expects.
+(define bedtools-for-ribotaper
+ (package (inherit bedtools)
+ (name "bedtools")
+ (version "2.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/arq5x/bedtools2/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))))
+
+(define-public ribotaper
+ (package
+ (name "ribotaper")
+ (version "1.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://ohlerlab.mdc-berlin.de/"
+ "files/RiboTaper/RiboTaper_Version_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("bedtools" ,bedtools-for-ribotaper)
+ ("samtools" ,samtools-0.1)
+ ("r" ,r)
+ ("r-foreach" ,r-foreach)
+ ("r-xnomial" ,r-xnomial)
+ ("r-domc" ,r-domc)
+ ("r-multitaper" ,r-multitaper)
+ ("r-seqinr" ,r-seqinr)))
+ (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
+ (synopsis "Define translated ORFs using ribosome profiling data")
+ (description
+ "RiboTaper is a method for defining translated ORFs using ribosome
+profiling data.")
+ (license license:gpl3+)))
+
(define-public bioawk
(package
(name "bioawk")
--
2.8.4