Subject: [PATCH 10/10] gnu: r-ggbio: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Wed, 23 Dec 2020 19:06:35 +0100

* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
---
 gnu/packages/bioconductor.scm   | 65 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 65 ---------------------------------
 2 files changed, 65 insertions(+), 65 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a3dd93e763..55df9bf7d1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,71 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
 by Ernst and Kellis.")
     (license license:artistic2.0)))
 
+(define-public r-ggbio
+  (package
+    (name "r-ggbio")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ggbio" version))
+       (sha256
+        (base32
+         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/tengfei/ggbio/issues/117
+         ;; This fix will be included in the next release.
+         (add-after 'unpack 'fix-typo
+           (lambda _
+             (substitute* "R/GGbio-class.R"
+               (("fechable") "fetchable"))
+             #t)))))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggally" ,r-ggally)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-gtable" ,r-gtable)
+       ("r-hmisc" ,r-hmisc)
+       ("r-iranges" ,r-iranges)
+       ("r-organismdbi" ,r-organismdbi)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "http://www.tengfei.name/ggbio/")
+    (synopsis "Visualization tools for genomic data")
+    (description
+     "The ggbio package extends and specializes the grammar of graphics for
+biological data.  The graphics are designed to answer common scientific
+questions, in particular those often asked of high throughput genomics data.
+All core Bioconductor data structures are supported, where appropriate.  The
+package supports detailed views of particular genomic regions, as well as
+genome-wide overviews.  Supported overviews include ideograms and grand linear
+views.  High-level plots include sequence fragment length, edge-linked
+interval to data view, mismatch pileup, and several splicing summaries.")
+    (license license:artistic2.0)))
+
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc483e6f13..512abcd8fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10484,71 +10484,6 @@ high-level packages for biological data visualization.  This saves development
 effort and encourages consistency.")
     (license license:artistic2.0)))
 
-(define-public r-ggbio
-  (package
-    (name "r-ggbio")
-    (version "1.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ggbio" version))
-       (sha256
-        (base32
-         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; See https://github.com/tengfei/ggbio/issues/117
-         ;; This fix will be included in the next release.
-         (add-after 'unpack 'fix-typo
-           (lambda _
-             (substitute* "R/GGbio-class.R"
-               (("fechable") "fetchable"))
-             #t)))))
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggally" ,r-ggally)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gtable" ,r-gtable)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "http://www.tengfei.name/ggbio/")
-    (synopsis "Visualization tools for genomic data")
-    (description
-     "The ggbio package extends and specializes the grammar of graphics for
-biological data.  The graphics are designed to answer common scientific
-questions, in particular those often asked of high throughput genomics data.
-All core Bioconductor data structures are supported, where appropriate.  The
-package supports detailed views of particular genomic regions, as well as
-genome-wide overviews.  Supported overviews include ideograms and grand linear
-views.  High-level plots include sequence fragment length, edge-linked
-interval to data view, mismatch pileup, and several splicing summaries.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2