From: zimoun <zimon.toutoune@gmail.com>
To: 45399@debbugs.gnu.org
Subject: [bug#45399] [PATCH 10/10] gnu: r-ggbio: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:35 +0100 [thread overview]
Message-ID: <20201223180635.58647-11-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com>
* 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
next prev parent reply other threads:[~2020-12-23 18:08 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-12-23 18:03 [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 01/10] gnu: r-sushi: Move " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 02/10] gnu: r-gwascat: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 03/10] gnu: r-gviz: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 05/10] gnu: r-ldblock: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 06/10] gnu: r-erma: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 08/10] gnu: r-snpstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06 ` zimoun [this message]
2020-12-29 16:42 ` bug#45399: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2020-12-30 9:13 ` [bug#45399] " zimoun
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