Subject: [bug#48575] [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Fri, 21 May 2021 22:26:22 +0200

* 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