From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <66914@debbugs.gnu.org>
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: [bug#66914] [PATCH 1/2] gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
Date: Fri, 3 Nov 2023 14:40:59 +0100 [thread overview]
Message-ID: <fcb3821b9f4004beecb10c285fbfd4dd58d0c1b6.1699018860.git.madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <c0f88b27-2a37-41a0-acf3-75ab334ff358@mdc-berlin.de>
* 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 d79236ea26..ac09a079b4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor)
\f
;;; 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-mafh5-gnomad-v3-1-2-grch38
(package
(name "r-mafh5-gnomad-v3-1-2-grch38")
base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d
--
2.41.0
next prev parent reply other threads:[~2023-11-03 13:42 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-11-03 13:30 [bug#66914] Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb Mădălin Ionel Patrașcu
2023-11-03 13:40 ` Mădălin Ionel Patrașcu [this message]
2023-11-03 13:41 ` [bug#66914] [PATCH 2/2] gnu: Add r-dnamcrosshyb Mădălin Ionel Patrașcu
2023-11-04 15:29 ` bug#66914: [PATCH 1/2] gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked Ricardo Wurmus
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