GNU bug report logs - #57340
[PATCH] gnu: Add r-organism-dplyr.

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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: [PATCH] gnu: Add r-organism-dplyr.
Date: Mon, 22 Aug 2022 13:26:27 +0200

* gnu/packages/bioconductor.scm (r-organism-dplyr): New variable.
---
 gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7d2ca413e9..ed9e4df73d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5017,6 +5017,45 @@ (define-public r-mzr
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
+(define-public r-organism-dplyr
+  (package
+    (name "r-organism-dplyr")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Organism.dplyr" version))
+       (sha256
+        (base32
+         "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
+    (properties `((upstream-name . "Organism.dplyr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi
+           r-annotationfilter
+           r-biocfilecache
+           r-dbi
+           r-dbplyr
+           r-dplyr
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-rlang
+           r-rsqlite
+           r-s4vectors
+           r-tibble))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/Organism.dplyr")
+    (synopsis "Dplyr-based access to Bioconductor annotation resources")
+    (description
+     "This package provides an alternative interface to Bioconductor @code{
+annotation} resources, in particular the gene identifier mapping functionality
+of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
+functionality of the @code{TxDb} packages (e.g.,
+@code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
+    (license license:artistic2.0)))
+
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")

base-commit: 706b3ef38b2f7ce9f05aa56e2eaaaf1c19e25f90
-- 
2.37.2

Message #10 received at 57340-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: 57340-done <at> debbugs.gnu.org
Subject: Re: [bug#57340] [PATCH] gnu: Add r-organism-dplyr.
Date: Tue, 23 Aug 2022 12:05:09 +0200

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

> * gnu/packages/bioconductor.scm (r-organism-dplyr): New variable.

Applied, thank you!

-- 
Ricardo

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