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02/07: gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.
From: |
Ricardo Wurmus |
Subject: |
02/07: gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked. |
Date: |
Fri, 15 Jun 2018 01:43:30 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit dfac7eb9170ae3b93ca2c179c13b33bc1ae7023d
Author: Ricardo Wurmus <address@hidden>
Date: Fri Jun 15 07:26:48 2018 +0200
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked):
New variable.
---
gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3dba9cb..7685cee 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")
- branch master updated (b494bbe -> 6ffdfe6), Ricardo Wurmus, 2018/06/15
- 01/07: gnu: Add r-bayseq., Ricardo Wurmus, 2018/06/15
- 04/07: gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked., Ricardo Wurmus, 2018/06/15
- 06/07: gnu: Add r-riboprofiling., Ricardo Wurmus, 2018/06/15
- 07/07: gnu: Add r-riboseqr., Ricardo Wurmus, 2018/06/15
- 05/07: gnu: Add r-chipcomp., Ricardo Wurmus, 2018/06/15
- 03/07: gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked., Ricardo Wurmus, 2018/06/15
- 02/07: gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.,
Ricardo Wurmus <=