gnu: r-rsamtools: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here.master
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@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web
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browser.")
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browser.")
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(license license:artistic2.0)))
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(license license:artistic2.0)))
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(define-public r-rsamtools
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(package
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(name "r-rsamtools")
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(version "2.6.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "Rsamtools" version))
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(sha256
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(base32
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"040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
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(properties
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`((upstream-name . "Rsamtools")))
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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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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biocparallel" ,r-biocparallel)
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("r-biostrings" ,r-biostrings)
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("r-bitops" ,r-bitops)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-rhtslib" ,r-rhtslib)
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("r-s4vectors" ,r-s4vectors)
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("r-xvector" ,r-xvector)))
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(home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
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(synopsis "Interface to samtools, bcftools, and tabix")
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(description
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"This package provides an interface to the @code{samtools},
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@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
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Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
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tab-delimited (tabix) files.")
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(license license:expat)))
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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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@ -7691,49 +7691,6 @@ including VCF header and contents in RDF and JSON.")
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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-rsamtools
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(package
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(name "r-rsamtools")
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(version "2.6.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "Rsamtools" version))
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(sha256
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(base32
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"040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
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(properties
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`((upstream-name . "Rsamtools")))
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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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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biocparallel" ,r-biocparallel)
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("r-biostrings" ,r-biostrings)
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("r-bitops" ,r-bitops)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-rhtslib" ,r-rhtslib)
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("r-s4vectors" ,r-s4vectors)
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("r-xvector" ,r-xvector)))
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(home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
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(synopsis "Interface to samtools, bcftools, and tabix")
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(description
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"This package provides an interface to the @code{samtools},
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@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
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Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
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tab-delimited (tabix) files.")
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(license license:expat)))
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(define-public r-delayedarray
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(define-public r-delayedarray
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(package
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(package
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(name "r-delayedarray")
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(name "r-delayedarray")
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