Mădălin Ionel Patrașcu wrote 1 years ago
(address . guix-patches@gnu.org)
c0f88b27-2a37-41a0-acf3-75ab334ff358@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked
and r-dnamcrosshyb): New variables.
Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.
- Done
Details
- 2 participants
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- Mădălin Ionel Patrașcu
- Severity
- normal
Mădălin Ionel Patrașcu wrote 1 years ago
[PATCH 2/2] gnu: Add r-dnamcrosshyb.
(address . 66914@debbugs.gnu.org)
045773685530dae0ff4ea375c219efc35f62a23b.1699018860.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-dnamcrosshyb): New variable.
Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
Toggle diff (58 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ac09a079b4..d5d5e9d25d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12636,6 +12636,51 @@ (define-public r-dnabarcodes
demultiplexed, i.e. assigned to their original reference barcode.")
(license license:gpl2)))
+;; It depends on Bioconductor packages
+(define-public r-dnamcrosshyb
+ ;; There aren't any releases.
+ (let ((commit "fe8acb33667e81f00dcb84e0fa75c87ab2db5d8f")
+ (revision "1"))
+ (package
+ (name "r-dnamcrosshyb")
+ (version (git-version "0.0.0.9000" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjhop/DNAmCrosshyb")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "12j1xsiqpvny5rp23z1az0k4cj5ajbcwkg65z00s16vywi2rx6nb"))))
+ (properties `((upstream-name . "DNAmCrosshyb")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome-hsapiens-ucsc-hg19-masked
+ r-bsgenome-hsapiens-ucsc-hg38-masked
+ r-dplyr
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-magrittr
+ r-minfi
+ r-purrr
+ r-s4vectors
+ r-shiny
+ r-stringi
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-watermelon))
+ (home-page "https://github.com/pjhop/DNAmCrosshyb")
+ (synopsis "DNAmCrosshyb")
+ (description
+ "Helper functions to detect cross-hybridization on Illumina DNAm arrays")
+ (license license:gpl3))))
+
(define-public r-ruvseq
(package
(name "r-ruvseq")
--
2.41.0
Mădălin Ionel Patrașcu wrote 1 years ago
[PATCH 1/2] gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
(address . 66914@debbugs.gnu.org)
fcb3821b9f4004beecb10c285fbfd4dd58d0c1b6.1699018860.git.madalinionel.patrascu@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(+)
Toggle diff (51 lines)
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)
;;; 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
Ricardo Wurmus wrote 1 years ago
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 66914-done@debbugs.gnu.org)
87jzqxsfih.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
Toggle quote (3 lines)
> * gnu/packages/bioconductor.scm
> (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.
I applied this series after moving r-dnamcrosshyb to (gnu packages
bioinformatics) because it is neither a CRAN nor Bioconductor package.
Thank you!
--
Ricardo
Closed
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