From 7bc5d1b0e1f1265028f221a51d7ee1c526132f65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 6 Mar 2019 21:33:17 +0100 Subject: gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor). * 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. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1bb1871fd0..a4e436e61d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -507,6 +507,41 @@ is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The 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 -- cgit v1.2.3