From: zimoun <zimon.toutoune@gmail.com>
To: 48575@debbugs.gnu.org.
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#48575] [PATCH 12/50] gnu: r-genomation: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:25:44 +0200 [thread overview]
Message-ID: <20210521202622.26591-12-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
---
gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 48 ---------------------------------
2 files changed, 48 insertions(+), 48 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eb73909723..2be7920770 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2099,6 +2099,54 @@ CAGE.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
+(define-public r-genomation
+ (package
+ (name "r-genomation")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomation" version))
+ (sha256
+ (base32
+ "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-data-table" ,r-data-table)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridbase" ,r-gridbase)
+ ("r-impute" ,r-impute)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plotrix" ,r-plotrix)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-runit" ,r-runit)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqpattern" ,r-seqpattern)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Summary, annotation and visualization of genomic data")
+ (description
+ "This package provides a package for summary and annotation of genomic
+intervals. Users can visualize and quantify genomic intervals over
+pre-defined functional regions, such as promoters, exons, introns, etc. The
+genomic intervals represent regions with a defined chromosome position, which
+may be associated with a score, such as aligned reads from HT-seq experiments,
+TF binding sites, methylation scores, etc. The package can use any tabular
+genomic feature data as long as it has minimal information on the locations of
+genomic intervals. In addition, it can use BAM or BigWig files as input.")
+ (license license:artistic2.0)))
+
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71f07748b6..f8e7b2cab9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,54 +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-genomation
- (package
- (name "r-genomation")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "genomation" version))
- (sha256
- (base32
- "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-data-table" ,r-data-table)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridbase" ,r-gridbase)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-plotrix" ,r-plotrix)
- ("r-plyr" ,r-plyr)
- ("r-rcpp" ,r-rcpp)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-runit" ,r-runit)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqpattern" ,r-seqpattern)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
- (synopsis "Summary, annotation and visualization of genomic data")
- (description
- "This package provides a package for summary and annotation of genomic
-intervals. Users can visualize and quantify genomic intervals over
-pre-defined functional regions, such as promoters, exons, introns, etc. The
-genomic intervals represent regions with a defined chromosome position, which
-may be associated with a score, such as aligned reads from HT-seq experiments,
-TF binding sites, methylation scores, etc. The package can use any tabular
-genomic feature data as long as it has minimal information on the locations of
-genomic intervals. In addition, it can use BAM or BigWig files as input.")
- (license license:artistic2.0)))
-
(define-public r-genomationdata
(package
(name "r-genomationdata")
--
2.30.1
next prev parent reply other threads:[~2021-05-21 20:28 UTC|newest]
Thread overview: 52+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-05-21 20:21 [bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 02/50] gnu: r-rtracklayer: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 04/50] gnu: r-topgo: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 05/50] gnu: r-bsgenome: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 06/50] gnu: r-msnid: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 07/50] gnu: r-msnbase: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 08/50] gnu: r-samr: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 09/50] gnu: r-impute: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 10/50] gnu: r-seqpattern: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 11/50] gnu: r-go-db: " zimoun
2021-05-21 20:25 ` zimoun [this message]
2021-05-21 20:25 ` [bug#48575] [PATCH 13/50] gnu: r-genomationdata: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 14/50] gnu: r-pcamethods: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 15/50] gnu: r-mzid: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 16/50] gnu: r-aroma-light: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 17/50] gnu: r-deseq: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 18/50] gnu: r-edaseq: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 19/50] gnu: r-interactivedisplaybase: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 20/50] gnu: r-annotationhub: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 21/50] gnu: r-fastseg: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 22/50] gnu: r-affy: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 23/50] gnu: r-keggrest: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 24/50] gnu: r-gage: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 25/50] gnu: r-complexheatmap: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 26/50] gnu: r-genomicfiles: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 27/50] gnu: r-dirichletmultinomial: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 28/50] gnu: r-organismdbi: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 29/50] gnu: r-affyio: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 30/50] gnu: r-vsn: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 31/50] gnu: r-biovizbase: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 32/50] gnu: r-ensembldb: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 33/50] gnu: r-mzr: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 34/50] gnu: r-protgenerics: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 35/50] gnu: r-sva: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 36/50] gnu: r-motifrg: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 37/50] gnu: r-seqlogo: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 38/50] gnu: r-zlibbioc: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 39/50] gnu: r-rhtslib: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 40/50] gnu: r-bamsignals: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 41/50] gnu: r-rcas: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 43/50] gnu: r-tximport: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 44/50] gnu: r-rhdf5filters: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 45/50] gnu: r-annotationfilter: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 46/50] gnu: r-rhdf5: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 47/50] gnu: r-chipseq: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 48/50] gnu: r-copyhelper: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 49/50] gnu: r-copywriter: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 50/50] gnu: r-methylkit: " zimoun
2021-05-31 14:07 ` bug#48575: [PATCH 00/50] Move some Bioconductor packages " Ricardo Wurmus
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