GNU bug report logs - #66914
Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.
Date: Fri, 3 Nov 2023 14:30:52 +0100

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked 
and r-dnamcrosshyb): New variables.

Message #8 received at 66914 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66914 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-dnamcrosshyb.
Date: Fri, 3 Nov 2023 14:41:00 +0100

* gnu/packages/bioconductor.scm (r-dnamcrosshyb): New variable.

Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873
---
 gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

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

Message #11 received at 66914 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66914 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
Date: Fri, 3 Nov 2023 14:40:59 +0100

* 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)
 
 ;;; 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

Message #16 received at 66914-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 66914-done <at> debbugs.gnu.org
Subject: Re: [bug#66914] [PATCH 1/2] gnu: Add
 r-bsgenome-hsapiens-ucsc-hg38-masked.
Date: Sat, 04 Nov 2023 16:29:21 +0100

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * 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

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