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authorRicardo Wurmus <rekado@elephly.net>2018-06-15 07:27:10 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-06-15 07:43:22 +0200
commit6fbd759b132d65825bfeb47ac66a957bde38c770 (patch)
tree55039489717962e227beef814399751e5923c742
parentdfac7eb9170ae3b93ca2c179c13b33bc1ae7023d (diff)
gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New variable.
-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 7685cee9e5..e1a1ba1963 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -96,6 +96,41 @@ 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-bsgenome-hsapiens-ucsc-hg19-masked
+ (package
+ (name "r-bsgenome-hsapiens-ucsc-hg19-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.Hsapiens.UCSC.hg19.masked_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
+ (properties
+ `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19"
+ ,r-bsgenome-hsapiens-ucsc-hg19)))
+ (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
+ (synopsis "Full masked genome sequences for Homo sapiens")
+ (description
+ "This package provides full genome sequences for Homo sapiens (Human) as
+provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
+sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, 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")