[PATCH] gnu: Add r-mutationalpatterns.

[PATCH] gnu: Add r-mutationalpatterns.

[Roel Janssen]

Dear Guix,

The following patch adds another bioinformatics-related R package.

Kind regards,
Roel Janssen


From 92a36d068c90c96b2b5b4a7c8b4578ac3f6255cd Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 27 Oct 2016 17:06:07 +0200
Subject: [PATCH] gnu: Add r-mutationalpatterns.

* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa35531..09bfb9d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7394,6 +7394,40 @@ library implementing most of the pipeline's features.")
 @dfn{RNA-centric annotation system} (RCAS).")
     (license license:agpl3+)))
 
+(define-public r-mutationalpatterns
+  (package
+    (name "r-mutationalpatterns")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MutationalPatterns" version))
+       (sha256
+        (base32
+         "1a3c2bm0xx0q4gf98jiw74msmdf2fr8rbsdysd5ww9kqlzmsbr17"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-iranges" ,r-iranges)
+       ("r-nmf" ,r-nmf)
+       ("r-plyr" ,r-plyr)
+       ("r-pracma" ,r-pracma)
+       ("r-reshape2" ,r-reshape2)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "http://bioconductor.org/packages/MutationalPatterns/")
+    (synopsis "Package for extracting and visualizing mutational patterns in
+SNV data")
+    (description "This package provides an extensive toolset for the
+characterization and visualization of a wide range of mutational patterns
+in base substitution data.")
+    (license license:expat)))
+
 (define-public emboss
   (package
     (name "emboss")
-- 
2.10.1

Re: [PATCH] gnu: Add r-mutationalpatterns.

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

>From 92a36d068c90c96b2b5b4a7c8b4578ac3f6255cd Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Thu, 27 Oct 2016 17:06:07 +0200
> Subject: [PATCH] gnu: Add r-mutationalpatterns.
>
> * gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.

[…]

> +    (synopsis "Package for extracting and visualizing mutational patterns in
> +SNV data")

This is a bit long.  How about this:

  “Extract and visualize mutational patterns in genomic data.”

> +    (description "This package provides an extensive toolset for the
> +characterization and visualization of a wide range of mutational patterns
> +in base substitution data.")

You could add a definition for “SNV” here so that the package will be
found when searching for “SNV” or its expansion.

Okay with these changes.  Thanks!

~~ Ricardo

Re: [PATCH] gnu: Add r-mutationalpatterns.

[Roel Janssen]

Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>
>>From 92a36d068c90c96b2b5b4a7c8b4578ac3f6255cd Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Thu, 27 Oct 2016 17:06:07 +0200
>> Subject: [PATCH] gnu: Add r-mutationalpatterns.
>>
>> * gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
>
> […]
>
>> +    (synopsis "Package for extracting and visualizing mutational patterns in
>> +SNV data")
>
> This is a bit long.  How about this:
>
>   “Extract and visualize mutational patterns in genomic data.”
>
>> +    (description "This package provides an extensive toolset for the
>> +characterization and visualization of a wide range of mutational patterns
>> +in base substitution data.")
>
> You could add a definition for “SNV” here so that the package will be
> found when searching for “SNV” or its expansion.
>
> Okay with these changes.  Thanks!
>
> ~~ Ricardo

Pushed with these changes at 7500e42b3.

Thanks!

Kind regards,
Roel Janssen