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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-06-15 07:26:48 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-06-15 07:43:22 +0200 |
| commit | dfac7eb9170ae3b93ca2c179c13b33bc1ae7023d (patch) | |
| tree | 62771eac52dc634fe104118b74b0e00498d65383 /gnu/packages | |
| parent | bb15b581f74dbf4f06425e3ef0aae1863adca377 (diff) | |
| download | patches-dfac7eb9170ae3b93ca2c179c13b33bc1ae7023d.tar patches-dfac7eb9170ae3b93ca2c179c13b33bc1ae7023d.tar.gz | |
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked):
New variable.
Diffstat (limited to 'gnu/packages')
| -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 3dba9cbab4..7685cee9e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -61,6 +61,41 @@ melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked + (package + (name "r-bsgenome-dmelanogaster-ucsc-dm3-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.Dmelanogaster.UCSC.dm3.masked_" + version ".tar.gz")) + (sha256 + (base32 + "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) + (properties + `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-dmelanogaster-ucsc-dm3" + ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") + (synopsis "Full masked genome sequences for Fly") + (description + "This package provides full masked genome sequences for Drosophila +melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in +Biostrings objects. The sequences are the same as in +BSgenome.Dmelanogaster.UCSC.dm3, 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") |