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gnu: r-genomicalignments: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here... * gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
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@ -1,5 +1,5 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
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;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
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;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
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@ -2280,6 +2280,39 @@ (define-public r-genomeinfodb
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names in their natural, rather than lexicographic, order.")
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names in their natural, rather than lexicographic, order.")
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(license license:artistic2.0)))
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(license license:artistic2.0)))
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(define-public r-genomicalignments
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(package
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(name "r-genomicalignments")
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(version "1.26.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "GenomicAlignments" version))
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(sha256
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(base32
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"1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
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(properties
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`((upstream-name . "GenomicAlignments")))
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(build-system r-build-system)
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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-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-rsamtools" ,r-rsamtools)
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("r-s4vectors" ,r-s4vectors)
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("r-summarizedexperiment" ,r-summarizedexperiment)))
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(home-page "https://bioconductor.org/packages/GenomicAlignments")
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(synopsis "Representation and manipulation of short genomic alignments")
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(description
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"This package provides efficient containers for storing and manipulating
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short genomic alignments (typically obtained by aligning short reads to a
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reference genome). This includes read counting, computing the coverage,
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junction detection, and working with the nucleotide content of the
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alignments.")
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(license license:artistic2.0)))
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(define-public r-genomicranges
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(define-public r-genomicranges
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(package
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(package
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(name "r-genomicranges")
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(name "r-genomicranges")
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@ -7952,39 +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-genomicalignments
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(package
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(name "r-genomicalignments")
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(version "1.26.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "GenomicAlignments" version))
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(sha256
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(base32
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"1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
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(properties
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`((upstream-name . "GenomicAlignments")))
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(build-system r-build-system)
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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-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-rsamtools" ,r-rsamtools)
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("r-s4vectors" ,r-s4vectors)
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("r-summarizedexperiment" ,r-summarizedexperiment)))
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(home-page "https://bioconductor.org/packages/GenomicAlignments")
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(synopsis "Representation and manipulation of short genomic alignments")
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(description
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"This package provides efficient containers for storing and manipulating
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short genomic alignments (typically obtained by aligning short reads to a
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reference genome). This includes read counting, computing the coverage,
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junction detection, and working with the nucleotide content of the
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alignments.")
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(license license:artistic2.0)))
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(define-public r-rtracklayer
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(define-public r-rtracklayer
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(package
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(package
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(name "r-rtracklayer")
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(name "r-rtracklayer")
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