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
next prev 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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