From: zimoun <zimon.toutoune@gmail.com>
To: 48575@debbugs.gnu.org.
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#48575] [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:26:22 +0200 [thread overview]
Message-ID: <20210521202622.26591-50-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
---
gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 47 ---------------------------------
2 files changed, 47 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe91fd486f..54a6afcf3d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3102,6 +3102,53 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-methylkit
+ (package
+ (name "r-methylkit")
+ (version "1.16.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylKit" version))
+ (sha256
+ (base32
+ "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
+ (properties `((upstream-name . "methylKit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-emdbook" ,r-emdbook)
+ ("r-fastseg" ,r-fastseg)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-mclust" ,r-mclust)
+ ("r-mgcv" ,r-mgcv)
+ ("r-qvalue" ,r-qvalue)
+ ("r-r-utils" ,r-r-utils)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://github.com/al2na/methylKit")
+ (synopsis
+ "DNA methylation analysis from high-throughput bisulfite sequencing results")
+ (description
+ "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing. The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing. It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+ (license license:artistic2.0)))
+
(define-public r-motifrg
(package
(name "r-motifrg")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 79146f915f..48b521f755 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,53 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-methylkit
- (package
- (name "r-methylkit")
- (version "1.16.1")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "methylKit" version))
- (sha256
- (base32
- "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
- (properties `((upstream-name . "methylKit")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-emdbook" ,r-emdbook)
- ("r-fastseg" ,r-fastseg)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-limma" ,r-limma)
- ("r-mclust" ,r-mclust)
- ("r-mgcv" ,r-mgcv)
- ("r-qvalue" ,r-qvalue)
- ("r-r-utils" ,r-r-utils)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
- (home-page "https://github.com/al2na/methylKit")
- (synopsis
- "DNA methylation analysis from high-throughput bisulfite sequencing results")
- (description
- "MethylKit is an R package for DNA methylation analysis and annotation
-from high-throughput bisulfite sequencing. The package is designed to deal
-with sequencing data from @dfn{Reduced representation bisulfite
-sequencing} (RRBS) and its variants, but also target-capture methods and whole
-genome bisulfite sequencing. It also has functions to analyze base-pair
-resolution 5hmC data from experimental protocols such as oxBS-Seq and
-TAB-Seq.")
- (license license:artistic2.0)))
-
(define-public r-raremetals2
(package
(name "r-raremetals2")
--
2.30.1
next prev parent reply other threads:[~2021-05-21 20:33 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 ` [bug#48575] [PATCH 12/50] gnu: r-genomation: " zimoun
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 ` zimoun [this message]
2021-05-31 14:07 ` bug#48575: [PATCH 00/50] Move some Bioconductor packages " Ricardo Wurmus
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