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authorRicardo Wurmus <rekado@elephly.net>2018-06-15 07:26:48 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-06-15 07:43:22 +0200
commitdfac7eb9170ae3b93ca2c179c13b33bc1ae7023d (patch)
tree62771eac52dc634fe104118b74b0e00498d65383
parentbb15b581f74dbf4f06425e3ef0aae1863adca377 (diff)
downloadpatches-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.
-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 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")