[PATCH] gnu: Add r-variantannotation.

[PATCH] gnu: Add r-variantannotation.

[Roel Janssen]

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From b973ee57f42e1e094d3dc377a5175de6ed252bc4 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 30 Mar 2016 15:03:56 +0200
Subject: [PATCH 1/2] gnu: Add r-variantannotation.

* gnu/packages/bioinformatics.scm (r-variantannotation): New variable.
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 887f6cc..79990a4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4040,6 +4040,38 @@ translation between different chromosome sequence naming conventions (e.g.,
 names in their natural, rather than lexicographic, order.")
     (license license:artistic2.0)))
 
+(define-public r-variantannotation
+  (package
+    (name "r-variantannotation")
+    (version "1.16.4")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "VariantAnnotation" version))
+              (sha256
+               (base32
+                "1z42j3p9b8h725inq8n0230llsdbav3gwcxy1nliypzfkxbzahsb"))))
+    (properties
+     `((upstream-name . "VariantAnnotation")))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/VariantAnnotation")
+    (synopsis "Package for annotation of genetic variants")
+    (description "This R package can annotate variants, compute amino acid
+coding changes and predict coding outcomes.")
+    (license license:artistic2.0)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
-- 
2.5.5


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From 38099e08370f84d589cdc7a486807c44f160949e Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 30 Mar 2016 15:05:31 +0200
Subject: [PATCH 2/2] gnu: Add r-zlibbioc.

* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.
---
 gnu/packages/bioinformatics.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 79990a4..5f3d5d5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4777,6 +4777,25 @@ identify genotyping errors, and to perform single-QTL and two-QTL,
 two-dimensional genome scans.")
   (license license:gpl3)))
 
+(define-public r-zlibbioc
+  (package
+    (name "r-zlibbioc")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "zlibbioc" version))
+              (sha256
+               (base32
+                "01wc26ndg4jsn1wyrl6zzq636gxaip5fci0xapym4lh9wryc4wnw"))))
+    (properties
+     `((upstream-name . "zlibbioc")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/zlibbioc")
+    (synopsis "Provider for zlib-1.2.5 to R packages")
+    (description "This package uses the source code of zlib-1.2.5 to create
+libraries for systems that do not have these available via other means.")
+    (license license:artistic2.0)))
+
 (define-public pepr
   (package
     (name "pepr")
-- 
2.5.5


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Dear Guix,

I want to add another R package: VariantAnnotation.  For this I also had
to add another R package called "zlibbioc".

Even though we provide zlib in GNU Guix, and it also uses the zlib input
instead of zlib provided by this package, it is a required dependency of
VariantAnnotation.  Instead of customizing the VariantAnnotation package
(and deviate from upstream development), I believe this is a fairly nice
solution.

I hope this is fine with you.

Kind regards,
Roel Janssen

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

[Leo Famulari]

On Wed, Mar 30, 2016 at 03:16:42PM +0200, Roel Janssen wrote:
> * gnu/packages/bioinformatics.scm (r-variantannotation): New variable.
> * gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.

Thanks for the patches! They look good to me, so I applied them,
bringing HEAD to 9e3ba31c5.