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01/02: gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
From: |
guix-commits |
Subject: |
01/02: gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked. |
Date: |
Sat, 4 Nov 2023 11:31:06 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit cb0e60cccfa88ed642a947d146bdc3c0da8d31ec
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Fri Nov 3 14:40:59 2023 +0100
gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
* gnu/packages/bioconductor.scm
(r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.
Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
---
gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8ccc5f49b2..38f9ce64ab 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -68,6 +68,42 @@
;;; 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")