Patchwork gnu: Add Ribotaper.

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Submitter Ricardo Wurmus
Date July 7, 2016, 9:26 a.m.
Message ID <20160707092629.23884-2-ricardo.wurmus@mdc-berlin.de>
Download mbox | patch
Permalink /patch/13695/
State New
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Ricardo Wurmus - July 7, 2016, 9:26 a.m.
* gnu/packages/bioinformatics.scm (bedtools-for-ribotaper, ribotaper):
  New variables.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

Patch

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")