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gnu: r-rtracklayer: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
This commit is contained in:
zimoun 2021-05-21 22:25:34 +02:00 committed by Ricardo Wurmus
parent ca1a015777
commit a88230a1bc
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2 changed files with 48 additions and 48 deletions
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48
gnu/packages/bioconductor.scm
View file

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

48
gnu/packages/bioinformatics.scm
View file

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