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gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Move from here...
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
...to here.
This commit is contained in:
Ricardo Wurmus 2019-03-06 21:33:17 +01:00
parent 13dabd6947
commit 7bc5d1b0e1
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2 changed files with 35 additions and 35 deletions
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35
gnu/packages/bioconductor.scm
View file

@ -507,6 +507,41 @@ (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
database is exposed as a @code{TxDb} object.")
(license license:artistic2.0)))
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
(version "3.4.4")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"TxDb.Mmusculus.UCSC.mm10.knownGene_"
version ".tar.gz"))
(sha256
(base32
"01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
;; As this package provides little more than a very large data file it
;; doesn't make sense to build substitutes.
(arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
("r-annotationdbi" ,r-annotationdbi)))
(home-page
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
(synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
(description
"This package loads a TxDb object, which is an R interface to
prefabricated databases contained in this package. This package provides
the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
based on the knownGene track.")
(license license:artistic2.0)))
(define-public r-biocgenerics
(package

35
gnu/packages/bioinformatics.scm
View file

@ -8105,41 +8105,6 @@ (define-public r-seqlogo
Stephens (1990).")
(license license:lgpl2.0+)))
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
(version "3.4.4")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"TxDb.Mmusculus.UCSC.mm10.knownGene_"
version ".tar.gz"))
(sha256
(base32
"01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
;; As this package provides little more than a very large data file it
;; doesn't make sense to build substitutes.
(arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
("r-annotationdbi" ,r-annotationdbi)))
(home-page
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
(synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
(description
"This package loads a TxDb object, which is an R interface to
prefabricated databases contained in this package. This package provides
the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
based on the knownGene track.")
(license license:artistic2.0)))
(define-public r-motifrg
(package
(name "r-motifrg")