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authorzimoun <zimon.toutoune@gmail.com>2020-12-23 19:06:35 +0100
committerRicardo Wurmus <rekado@elephly.net>2020-12-29 17:40:28 +0100
commit610cd6a170474550dffd8a58eb3651ef10ca7f6e (patch)
tree607854b0a60ef70d51ab00ecc2343b27a65a4471 /gnu/packages/bioinformatics.scm
parent81f481d6cdbbd035c1642d9d257af6805f4d22dc (diff)
gnu: r-ggbio: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm65
1 files changed, 0 insertions, 65 deletions
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"))