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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-06-15 07:27:29 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-06-15 07:43:22 +0200 |
| commit | 2bece692a685d4a4e823cf908898a2aceaadc6c2 (patch) | |
| tree | 2f10bae5d9ad0b4ab4cb791365dfb37d5d7d97b3 /gnu/packages | |
| parent | 6fbd759b132d65825bfeb47ac66a957bde38c770 (diff) | |
| download | gnu-guix-2bece692a685d4a4e823cf908898a2aceaadc6c2.tar gnu-guix-2bece692a685d4a4e823cf908898a2aceaadc6c2.tar.gz | |
gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New
variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e1a1ba1963..e962ad523e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -131,6 +131,41 @@ Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) +(define-public r-bsgenome-mmusculus-ucsc-mm9-masked + (package + (name "r-bsgenome-mmusculus-ucsc-mm9-masked") + (version "1.3.99") + (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/" + "BSgenome.Mmusculus.UCSC.mm9.masked_" + version ".tar.gz")) + (sha256 + (base32 + "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) + (properties + `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-mmusculus-ucsc-mm9" + ,r-bsgenome-mmusculus-ucsc-mm9))) + (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") + (synopsis "Full masked genome sequences for Mouse") + (description + "This package provides full genome sequences for Mus musculus (Mouse) as +provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The +sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of +them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS +mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of +repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem +Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by +default." ) + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") |