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| -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 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") |