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gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.

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* gnu/packages/bioconductor.scm
  (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.

Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
This commit is contained in:
Mădălin Ionel Patrașcu 2023-11-03 14:40:59 +01:00 committed by Ricardo Wurmus
parent 9dcd8802f5
commit cb0e60cccf
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1 changed files with 36 additions and 0 deletions
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gnu/packages/bioconductor.scm
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@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor)
;;; Annotations
(define-public r-bsgenome-hsapiens-ucsc-hg38-masked
(package
(name "r-bsgenome-hsapiens-ucsc-hg38-masked")
(version "1.4.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version
'annotation))
(sha256
(base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"))))
(properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked")))
(build-system r-build-system)
(propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38
r-genomeinfodb))
(home-page
"https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked")
(synopsis
"Full masked genomic sequences for Homo sapiens (UCSC version hg38)")
(description
"This package provides the complete genome sequences for Homo sapiens as
provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each
of them has the 4 following masks on top:
@enumerate
@item the mask of assembly gaps (AGAPS mask);
@item the mask of intra-contig ambiguities (AMB mask);
@item the mask of repeats from @code{RepeatMasker} (RM mask);
@item the mask of repeats from Tandem Repeats Finder (TRF mask).
@end enumerate
Only the AGAPS and AMB masks are \"active\" by default. The sequences are stored
in @code{MaskedDNAString} objects.")
(license license:artistic2.0)))
(define-public r-hpo-db
(package
(name "r-hpo-db")