GNU bug report logs - #52463
[PATCH] gnu: Add r-chromvarmotifs.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#52463: closed ([PATCH] gnu: Add r-chromvarmotifs.)
Date: Mon, 13 Dec 2021 12:40:01 +0000

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Your message dated Mon, 13 Dec 2021 12:38:34 +0000
with message-id <87r1agn0fz.fsf <at> elephly.net>
and subject line [PATCH] gnu: Add r-chromvarmotifs.
has caused the debbugs.gnu.org bug report #52463,
regarding [PATCH] gnu: Add r-chromvarmotifs.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
52463: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=52463
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Contact help-debbugs <at> gnu.org with problems

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-chromvarmotifs.
Date: Mon, 13 Dec 2021 12:52:07 +0100

* gnu/packages/bioconductor.scm (r-chromvarmotifs): New variable.
This package is not a bioconductor one, but it use the r-tfbstools
that is stored in bioconductor.scm.  If I used the cran.scm for the
current definition I should import the bioconductor and it already
imports cran.  Beside this the package is somehow related with other
bioconductor packages.
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 44bf5c7d24..28cc8b7458 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1183,6 +1183,35 @@ (define-public r-chromstardata
 chromstaR package.")
     (license license:gpl3)))
 
+(define-public r-chromvarmotifs
+  (let
+      ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
+       (revision "1"))
+    (package
+      (name "r-chromvarmotifs")
+      (version (git-version "0.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/GreenleafLab/chromVARmotifs")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q"))))
+      (properties `((upstream-name . "chromVARmotifs")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-tfbstools" ,r-tfbstools)))
+      (home-page "https://github.com/GreenleafLab/chromVARmotifs")
+      (synopsis "Stores motif collections for use with motifmatchr or chromVAR")
+      (description
+       "This package @code{r-chromvarmotifs} stores motifs collections as
+lists of @dfn{position frequency matrix} (PWMatrixList) objects provided by
+@code{TFBSTools} package for use in R with packages like @code{motifmatchr} or
+@code{chromVAR}.")
+      (license license:expat))))
+
 (define-public r-copyhelper
   (package
     (name "r-copyhelper")
-- 
2.34.0

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 52463-done <at> debbugs.gnu.org
Cc: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-chromvarmotifs.
Date: Mon, 13 Dec 2021 12:38:34 +0000

Applied to the “master” branch with commit
5f32468acfc7ae3a7dd736810ab0c3cdde7310da.  Thanks!

-- 
Ricardo

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