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gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.

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* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New
variable.
This commit is contained in:
Ricardo Wurmus 2018-06-15 07:27:10 +02:00
parent dfac7eb917
commit 6fbd759b13
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gnu/packages/bioconductor.scm
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@ -96,6 +96,41 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
(license license:artistic2.0))) (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 (define-public r-hpar
(package (package
(name "r-hpar") (name "r-hpar")