Patchwork [2/2] gnu: Add r-bamsignals.

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Submitter Ricardo Wurmus
Date Aug. 18, 2016, 11:09 a.m.
Message ID <20160818110942.28804-2-ricardo.wurmus@mdc-berlin.de>
Download mbox | patch
Permalink /patch/14746/
State New
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Comments

Ricardo Wurmus - Aug. 18, 2016, 11:09 a.m.
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
Leo Famulari - Aug. 21, 2016, 8:27 p.m.
On Thu, Aug 18, 2016 at 01:09:42PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-bamsignals): New variable.

LGTM
Ricardo Wurmus - Aug. 22, 2016, 2:53 p.m.
Leo Famulari <leo@famulari.name> writes:

> On Thu, Aug 18, 2016 at 01:09:42PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
>
> LGTM

Thanks.  Pushed as fe02c4c98aee859f7eb75e7ca18a78498ba7fa78.

~~ Ricardo

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ade6e37..2bd71c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6350,6 +6350,36 @@  nucleotide sequence analysis.  The package is primarily useful to developers
 of other R packages who wish to make use of HTSlib.")
     (license license:lgpl2.0+)))
 
+(define-public r-bamsignals
+  (package
+    (name "r-bamsignals")
+    (version "1.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bamsignals" version))
+       (sha256
+        (base32
+         "1xqiqvg52p6fcvhr4146djbz79r3j1kmh75mq7rndwglmiybpwmy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "http://bioconductor.org/packages/bamsignals")
+    (synopsis "Extract read count signals from bam files")
+    (description
+     "This package allows to efficiently obtain count vectors from indexed bam
+files.  It counts the number of nucleotide sequence reads in given genomic
+ranges and it computes reads profiles and coverage profiles.  It also handles
+paired-end data.")
+    (license license:gpl2+)))
+
 (define-public emboss
   (package
     (name "emboss")