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

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* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
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zimoun 2021-05-21 22:26:04 +02:00 committed by Ricardo Wurmus
parent fea33b9d1e
commit 88cf24febb
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2 changed files with 45 additions and 45 deletions
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45
gnu/packages/bioconductor.scm
View file

@ -2603,6 +2603,51 @@ (define-public r-edger
CAGE.") CAGE.")
(license license:gpl2+))) (license license:gpl2+)))
(define-public r-ensembldb
(package
(name "r-ensembldb")
(version "2.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
"1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-annotationfilter" ,r-annotationfilter)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-curl" ,r-curl)
("r-dbi" ,r-dbi)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-protgenerics" ,r-protgenerics)
("r-rsamtools" ,r-rsamtools)
("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/jotsetung/ensembldb")
(synopsis "Utilities to create and use Ensembl-based annotation databases")
(description
"The package provides functions to create and use transcript-centric
annotation databases/packages. The annotation for the databases are directly
fetched from Ensembl using their Perl API. The functionality and data is
similar to that of the TxDb packages from the @code{GenomicFeatures} package,
but, in addition to retrieve all gene/transcript models and annotations from
the database, the @code{ensembldb} package also provides a filter framework
allowing to retrieve annotations for specific entries like genes encoded on a
chromosome region or transcript models of lincRNA genes.")
;; No version specified
(license license:lgpl3+)))
(define-public r-fastseg (define-public r-fastseg
(package (package
(name "r-fastseg") (name "r-fastseg")

45
gnu/packages/bioinformatics.scm
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@ -9108,51 +9108,6 @@ (define-public r-mzr
previously been used in XCMS.") previously been used in XCMS.")
(license license:artistic2.0))) (license license:artistic2.0)))
(define-public r-ensembldb
(package
(name "r-ensembldb")
(version "2.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
"1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-annotationfilter" ,r-annotationfilter)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-curl" ,r-curl)
("r-dbi" ,r-dbi)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-protgenerics" ,r-protgenerics)
("r-rsamtools" ,r-rsamtools)
("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/jotsetung/ensembldb")
(synopsis "Utilities to create and use Ensembl-based annotation databases")
(description
"The package provides functions to create and use transcript-centric
annotation databases/packages. The annotation for the databases are directly
fetched from Ensembl using their Perl API. The functionality and data is
similar to that of the TxDb packages from the @code{GenomicFeatures} package,
but, in addition to retrieve all gene/transcript models and annotations from
the database, the @code{ensembldb} package also provides a filter framework
allowing to retrieve annotations for specific entries like genes encoded on a
chromosome region or transcript models of lincRNA genes.")
;; No version specified
(license license:lgpl3+)))
(define-public r-dropbead (define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2")) (revision "2"))