Subject: [PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Fri, 21 May 2021 22:25:35 +0200

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
---
 gnu/packages/bioconductor.scm   | 43 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 43 ---------------------------------
 2 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 42a3d1fffc..2263c17cc4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the
 alignments.")
     (license license:artistic2.0)))
 
+(define-public r-genomicfeatures
+  (package
+    (name "r-genomicfeatures")
+    (version "1.42.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicFeatures" version))
+              (sha256
+               (base32
+                "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
+    (properties
+     `((upstream-name . "GenomicFeatures")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/GenomicFeatures")
+    (synopsis "Tools for working with transcript centric annotations")
+    (description
+     "This package provides a set of tools and methods for making and
+manipulating transcript centric annotations.  With these tools the user can
+easily download the genomic locations of the transcripts, exons and cds of a
+given organism, from either the UCSC Genome Browser or a BioMart
+database (more sources will be supported in the future).  This information is
+then stored in a local database that keeps track of the relationship between
+transcripts, exons, cds and genes.  Flexible methods are provided for
+extracting the desired features in a convenient format.")
+    (license license:artistic2.0)))
+
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9fb46c0d5d..bf8cb2f3a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,49 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomicfeatures
-  (package
-    (name "r-genomicfeatures")
-    (version "1.42.3")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicFeatures" version))
-              (sha256
-               (base32
-                "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
-    (properties
-     `((upstream-name . "GenomicFeatures")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/GenomicFeatures")
-    (synopsis "Tools for working with transcript centric annotations")
-    (description
-     "This package provides a set of tools and methods for making and
-manipulating transcript centric annotations.  With these tools the user can
-easily download the genomic locations of the transcripts, exons and cds of a
-given organism, from either the UCSC Genome Browser or a BioMart
-database (more sources will be supported in the future).  This information is
-then stored in a local database that keeps track of the relationship between
-transcripts, exons, cds and genes.  Flexible methods are provided for
-extracting the desired features in a convenient format.")
-    (license license:artistic2.0)))
-
 (define-public r-go-db
   (package
     (name "r-go-db")
-- 
2.30.1