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.
This commit is contained in:
zimoun
Ricardo Wurmus
parent
81f481d6cd
commit
610cd6a170
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@ -9308,6 +9308,71 @@ (define-public r-erma
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by Ernst and Kellis.")
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(license license:artistic2.0)))
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(define-public r-ggbio
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(package
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(name "r-ggbio")
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(version "1.38.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "ggbio" version))
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(sha256
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(base32
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"0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
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(build-system r-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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;; See https://github.com/tengfei/ggbio/issues/117
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;; This fix will be included in the next release.
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(add-after 'unpack 'fix-typo
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(lambda _
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(substitute* "R/GGbio-class.R"
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(("fechable") "fetchable"))
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#t)))))
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(propagated-inputs
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`(("r-annotationdbi" ,r-annotationdbi)
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("r-annotationfilter" ,r-annotationfilter)
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("r-biobase" ,r-biobase)
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("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-biovizbase" ,r-biovizbase)
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("r-bsgenome" ,r-bsgenome)
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("r-ensembldb" ,r-ensembldb)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-genomicranges" ,r-genomicranges)
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("r-ggally" ,r-ggally)
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("r-ggplot2" ,r-ggplot2)
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("r-gridextra" ,r-gridextra)
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("r-gtable" ,r-gtable)
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("r-hmisc" ,r-hmisc)
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("r-iranges" ,r-iranges)
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("r-organismdbi" ,r-organismdbi)
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("r-reshape2" ,r-reshape2)
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("r-rlang" ,r-rlang)
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("r-rsamtools" ,r-rsamtools)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-scales" ,r-scales)
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("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-variantannotation" ,r-variantannotation)))
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(native-inputs
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`(("r-knitr" ,r-knitr)))
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(home-page "http://www.tengfei.name/ggbio/")
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(synopsis "Visualization tools for genomic data")
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(description
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"The ggbio package extends and specializes the grammar of graphics for
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biological data. The graphics are designed to answer common scientific
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questions, in particular those often asked of high throughput genomics data.
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All core Bioconductor data structures are supported, where appropriate. The
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package supports detailed views of particular genomic regions, as well as
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genome-wide overviews. Supported overviews include ideograms and grand linear
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views. High-level plots include sequence fragment length, edge-linked
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interval to data view, mismatch pileup, and several splicing summaries.")
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(license license:artistic2.0)))
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(define-public r-gqtlbase
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(package
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(name "r-gqtlbase")
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@ -10484,71 +10484,6 @@ (define-public r-biovizbase
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effort and encourages consistency.")
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(license license:artistic2.0)))
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(define-public r-ggbio
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(package
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(name "r-ggbio")
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(version "1.38.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "ggbio" version))
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(sha256
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(base32
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"0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
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(build-system r-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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;; See https://github.com/tengfei/ggbio/issues/117
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;; This fix will be included in the next release.
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(add-after 'unpack 'fix-typo
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(lambda _
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(substitute* "R/GGbio-class.R"
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(("fechable") "fetchable"))
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#t)))))
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(propagated-inputs
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`(("r-annotationdbi" ,r-annotationdbi)
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("r-annotationfilter" ,r-annotationfilter)
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("r-biobase" ,r-biobase)
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("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-biovizbase" ,r-biovizbase)
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("r-bsgenome" ,r-bsgenome)
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("r-ensembldb" ,r-ensembldb)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-genomicranges" ,r-genomicranges)
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("r-ggally" ,r-ggally)
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("r-ggplot2" ,r-ggplot2)
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("r-gridextra" ,r-gridextra)
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("r-gtable" ,r-gtable)
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("r-hmisc" ,r-hmisc)
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("r-iranges" ,r-iranges)
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("r-organismdbi" ,r-organismdbi)
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("r-reshape2" ,r-reshape2)
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("r-rlang" ,r-rlang)
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("r-rsamtools" ,r-rsamtools)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-scales" ,r-scales)
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("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-variantannotation" ,r-variantannotation)))
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(native-inputs
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`(("r-knitr" ,r-knitr)))
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(home-page "http://www.tengfei.name/ggbio/")
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(synopsis "Visualization tools for genomic data")
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(description
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"The ggbio package extends and specializes the grammar of graphics for
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biological data. The graphics are designed to answer common scientific
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questions, in particular those often asked of high throughput genomics data.
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All core Bioconductor data structures are supported, where appropriate. The
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package supports detailed views of particular genomic regions, as well as
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genome-wide overviews. Supported overviews include ideograms and grand linear
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views. High-level plots include sequence fragment length, edge-linked
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interval to data view, mismatch pileup, and several splicing summaries.")
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(license license:artistic2.0)))
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(define-public r-dropbead
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(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
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(revision "2"))
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