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gnu: r-rtracklayer: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here... * gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
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ca1a015777
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2 changed files with 48 additions and 48 deletions
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@ -2590,6 +2590,54 @@ (define-public r-rsamtools
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tab-delimited (tabix) files.")
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tab-delimited (tabix) files.")
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(license license:expat)))
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(license license:expat)))
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(define-public r-rtracklayer
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(package
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(name "r-rtracklayer")
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(version "1.50.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "rtracklayer" version))
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(sha256
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(base32
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"12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
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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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(add-after 'unpack 'use-system-zlib
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(lambda _
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(substitute* "DESCRIPTION"
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((" zlibbioc,") ""))
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(substitute* "NAMESPACE"
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(("import\\(zlibbioc\\)") ""))
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#t)))))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(inputs
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`(("zlib" ,zlib)))
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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-rcurl" ,r-rcurl)
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("r-rsamtools" ,r-rsamtools)
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("r-s4vectors" ,r-s4vectors)
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("r-xml" ,r-xml)
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("r-xvector" ,r-xvector)
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("r-zlibbioc" ,r-zlibbioc)))
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(home-page "https://bioconductor.org/packages/rtracklayer")
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(synopsis "R interface to genome browsers and their annotation tracks")
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(description
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"rtracklayer is an extensible framework for interacting with multiple
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genome browsers (currently UCSC built-in) and manipulating annotation tracks
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in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
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built-in). The user may export/import tracks to/from the supported browsers,
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as well as query and modify the browser state, such as the current viewport.")
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(license license:artistic2.0)))
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(define-public r-shortread
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(define-public r-shortread
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(package
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(package
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(name "r-shortread")
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(name "r-shortread")
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@ -7952,54 +7952,6 @@ (define-public bio-vcf
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(home-page "https://github.com/vcflib/bio-vcf")
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(home-page "https://github.com/vcflib/bio-vcf")
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(license license:expat)))
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(license license:expat)))
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(define-public r-rtracklayer
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(package
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(name "r-rtracklayer")
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(version "1.50.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "rtracklayer" version))
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(sha256
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(base32
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"12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
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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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(add-after 'unpack 'use-system-zlib
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(lambda _
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(substitute* "DESCRIPTION"
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((" zlibbioc,") ""))
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(substitute* "NAMESPACE"
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(("import\\(zlibbioc\\)") ""))
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#t)))))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(inputs
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`(("zlib" ,zlib)))
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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-rcurl" ,r-rcurl)
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("r-rsamtools" ,r-rsamtools)
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("r-s4vectors" ,r-s4vectors)
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("r-xml" ,r-xml)
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("r-xvector" ,r-xvector)
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("r-zlibbioc" ,r-zlibbioc)))
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(home-page "https://bioconductor.org/packages/rtracklayer")
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(synopsis "R interface to genome browsers and their annotation tracks")
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(description
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"rtracklayer is an extensible framework for interacting with multiple
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genome browsers (currently UCSC built-in) and manipulating annotation tracks
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in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
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built-in). The user may export/import tracks to/from the supported browsers,
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as well as query and modify the browser state, such as the current viewport.")
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(license license:artistic2.0)))
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(define-public r-genomicfeatures
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(define-public r-genomicfeatures
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(package
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(package
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(name "r-genomicfeatures")
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(name "r-genomicfeatures")
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