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authorRicardo Wurmus <rekado@elephly.net>2018-06-15 07:27:29 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-06-15 07:43:22 +0200
commit2bece692a685d4a4e823cf908898a2aceaadc6c2 (patch)
tree2f10bae5d9ad0b4ab4cb791365dfb37d5d7d97b3 /gnu/packages
parent6fbd759b132d65825bfeb47ac66a957bde38c770 (diff)
downloadpatches-2bece692a685d4a4e823cf908898a2aceaadc6c2.tar
patches-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.scm35
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")