GNU bug report logs - #45399
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

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From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [bug#45399] [PATCH 03/10] gnu: r-gviz: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:28 +0100

* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
---
 gnu/packages/bioconductor.scm   | 49 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 49 ---------------------------------
 2 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 970602a32b..11e9a46b11 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,55 @@ preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
 
+(define-public r-gviz
+  (package
+    (name "r-gviz")
+    (version "1.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Gviz" version))
+       (sha256
+        (base32
+         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
+    (properties `((upstream-name . "Gviz")))
+    (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-biovizbase" ,r-biovizbase)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-digest" ,r-digest)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/Gviz")
+    (synopsis "Plotting data and annotation information along genomic coordinates")
+    (description
+     "Genomic data analyses requires integrated visualization of known genomic
+information and new experimental data.  Gviz uses the biomaRt and the
+rtracklayer packages to perform live annotation queries to Ensembl and UCSC
+and translates this to e.g. gene/transcript structures in viewports of the
+grid graphics package.  This results in genomic information plotted together
+with your data.")
+    (license license:artistic2.0)))
+
 (define-public r-gwascat
   (package
     (name "r-gwascat")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab187dcddd..caa505fdab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10785,55 +10785,6 @@ interpretation of members of a collection of association statistics on a
 family of feature/genome hypotheses.")
     (license license:artistic2.0)))
 
-(define-public r-gviz
-  (package
-    (name "r-gviz")
-    (version "1.34.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Gviz" version))
-       (sha256
-        (base32
-         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
-    (properties `((upstream-name . "Gviz")))
-    (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-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-digest" ,r-digest)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/Gviz")
-    (synopsis "Plotting data and annotation information along genomic coordinates")
-    (description
-     "Genomic data analyses requires integrated visualization of known genomic
-information and new experimental data.  Gviz uses the biomaRt and the
-rtracklayer packages to perform live annotation queries to Ensembl and UCSC
-and translates this to e.g. gene/transcript structures in viewports of the
-grid graphics package.  This results in genomic information plotted together
-with your data.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

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