From c5173d74d67b786c36dd53930c5d4fe4805cf3e9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 12 Jan 2017 10:02:57 +0100 Subject: gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene. * gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14daf59c92..d82b6c093c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7100,6 +7100,41 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10 in Biostrings objects.") (license license:artistic2.0))) +(define-public r-txdb-mmusculus-ucsc-mm10-knowngene + (package + (name "r-txdb-mmusculus-ucsc-mm10-knowngene") + (version "3.4.0") + (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 "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "TxDb.Mmusculus.UCSC.mm10.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb")))) + (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 + "http://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-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") -- cgit v1.2.3