* [PATCH] gnu: Add r-mutationalpatterns.
@ 2016-10-27 15:07 Roel Janssen
2016-10-27 17:22 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Roel Janssen @ 2016-10-27 15:07 UTC (permalink / raw
To: guix-devel
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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: Add r-mutationalpatterns.
2016-10-27 15:07 [PATCH] gnu: Add r-mutationalpatterns Roel Janssen
@ 2016-10-27 17:22 ` Ricardo Wurmus
2016-10-27 18:09 ` Roel Janssen
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2016-10-27 17:22 UTC (permalink / raw
To: Roel Janssen; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: Add r-mutationalpatterns.
2016-10-27 17:22 ` Ricardo Wurmus
@ 2016-10-27 18:09 ` Roel Janssen
0 siblings, 0 replies; 3+ messages in thread
From: Roel Janssen @ 2016-10-27 18:09 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 3+ messages in thread
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2016-10-27 15:07 [PATCH] gnu: Add r-mutationalpatterns Roel Janssen
2016-10-27 17:22 ` Ricardo Wurmus
2016-10-27 18:09 ` Roel Janssen
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