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From: zimoun <zimon.toutoune@gmail.com>
To: 47156@debbugs.gnu.org
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#47156] [PATCH 10/10] gnu: r-variantannotation: Move to (gnu packages bioconductor).
Date: Mon, 15 Mar 2021 14:01:58 +0100	[thread overview]
Message-ID: <20210315130158.30365-1-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210315125800.30246-1-zimon.toutoune@gmail.com>

* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
---
 gnu/packages/bioconductor.scm   | 38 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 38 ---------------------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fb0127b7ca..c4df090a05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2051,6 +2051,44 @@ experimental designs is facilitated by a consistently implemented sample
 annotation infrastructure.")
     (license license:artistic2.0)))
 
+(define-public r-variantannotation
+  (package
+    (name "r-variantannotation")
+    (version "1.36.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "VariantAnnotation" version))
+              (sha256
+               (base32
+                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
+    (properties
+     `((upstream-name . "VariantAnnotation")))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)
+       ("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-geneplotter
   (package
     (name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dc0d7a2906..78df3091fe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-variantannotation
-  (package
-    (name "r-variantannotation")
-    (version "1.36.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "VariantAnnotation" version))
-              (sha256
-               (base32
-                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
-    (properties
-     `((upstream-name . "VariantAnnotation")))
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)
-       ("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-limma
   (package
     (name "r-limma")
-- 
2.30.1





  parent reply	other threads:[~2021-03-15 13:03 UTC|newest]

Thread overview: 12+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-03-15 12:58 [bug#47156] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 02/10] gnu: r-biocviews: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 03/10] gnu: r-biocstyle: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 04/10] gnu: r-bioccheck: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 05/10] gnu: r-s4vectors: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 06/10] gnu: r-iranges: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 07/10] gnu: r-genomeinfodbdata: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 08/10] gnu: r-genomeinfodb: " zimoun
2021-03-15 13:01   ` [bug#47156] [PATCH 09/10] gnu: r-edger: " zimoun
2021-03-15 13:01 ` zimoun [this message]
2021-03-15 13:09 ` bug#47156: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus

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