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Re: [PATCH] gnu: Add r-limma.
From: |
Roel Janssen |
Subject: |
Re: [PATCH] gnu: Add r-limma. |
Date: |
Tue, 03 May 2016 12:25:18 +0200 |
User-agent: |
mu4e 0.9.17; emacs 25.1.50.3 |
Dear Ricardo,
Thanks for your quick response.
Ricardo Wurmus writes:
> Roel Janssen <address@hidden> writes:
>
>> Dear Guix,
>>
>> I have two R packages I would like to add. The other package 'r-edger'
>> depends on this one. This is the first time I'm attempting an inline
>> patch, so I hope this works out well.
>
> Thanks for the patch. It worked!
>
>>>From 565fa10f9896e1143419b2a2c6496b91a135a930 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <address@hidden>
>> Date: Tue, 3 May 2016 09:30:14 +0200
>> Subject: [PATCH] gnu: Add r-limma.
>>
>> * gnu/packages/bioinformatics.scm (r-limma): New variable.
>> ---
>> gnu/packages/bioinformatics.scm | 18 ++++++++++++++++++
>> 1 file changed, 18 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm
>> b/gnu/packages/bioinformatics.scm
>> index 079fd46..3dfb55e 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4171,6 +4171,24 @@ names in their natural, rather than lexicographic,
>> order.")
>> coding changes and predict coding outcomes.")
>> (license license:artistic2.0)))
>>
>> +(define-public r-limma
>> + (package
>> + (name "r-limma")
>> + (version "3.26.9")
>> + (source (origin
>> + (method url-fetch)
>> + (uri (bioconductor-uri "limma" version))
>> + (sha256
>> + (base32
>> + "0mj72zsj1awjf3i2y9x8m7ih4sx9qrs1rlrck9l7mn5afxqsfrsm"))))
>> + (properties `((upstream-name . "limma")))
>
> I don’t think we need this as the name is all lowercase, as expected.
> We only set the “upstream-name” property when the name contains special
> characters or uppercase letters.
Ok. I removed it from the second version of this patch.
>> + (build-system r-build-system)
>> + (home-page "http://bioinf.wehi.edu.au/limma")
>> + (synopsis "This package provides linear models for microarray data")
>> + (description "This package provides linear models and differential
>> +expression for microarray data analysis.")
>
> The description could be improved. There’s a better description on the
> home page. You might be able to adapt it.
Great, I adapted the text from the website.
Here's the new version of the patch:
>From a56362450a085d0b5d2730c52f4fed9200a24fb9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <address@hidden>
Date: Tue, 3 May 2016 12:22:50 +0200
Subject: [PATCH] gnu: Add r-limma.
* gnu/packages/bioinformatics.scm (r-limma): New variable.
---
gnu/packages/bioinformatics.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 079fd46..d6da0ac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4171,6 +4171,26 @@ names in their natural, rather than lexicographic,
order.")
coding changes and predict coding outcomes.")
(license license:artistic2.0)))
+(define-public r-limma
+ (package
+ (name "r-limma")
+ (version "3.26.9")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "limma" version))
+ (sha256
+ (base32
+ "0mj72zsj1awjf3i2y9x8m7ih4sx9qrs1rlrck9l7mn5afxqsfrsm"))))
+ (build-system r-build-system)
+ (home-page "http://bioinf.wehi.edu.au/limma")
+ (synopsis "This package provides linear models for microarray data")
+ (description "This package can be used for the analysis of gene expression
+studies, especially the use of linear models for analysing designed experiments
+and the assessment of differential expression. The analysis methods apply to
+many different technologies, including microarrays, RNA-seq, quantitative PCR
+and many protein technologies.")
+ (license license:gpl2+)))
+
(define-public r-xvector
(package
(name "r-xvector")
--
2.7.4