GNU bug report logs - #45282
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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>
Date: Wed, 16 Dec 2020 23:02:15 +0100

Message #8 received at 45282 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <45282 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 1/2] gnu: Add r-kegggraph.
Date: Wed, 16 Dec 2020 23:03:41 +0100

* gnu/packages/bioconductor.scm (r-kegggraph): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4a1af4306..3026d1a496 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9247,3 +9247,29 @@ graph with the mapped data.  In addition, @code{r-pathview} also seamlessly
 integrates with pathway and gene set (enrichment) analysis tools for
 large-scale and fully automated analysis.")
     (license license:gpl3+)))
+
+(define-public r-kegggraph
+  (package
+    (name "r-kegggraph")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "KEGGgraph" version))
+       (sha256
+        (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
+    (properties `((upstream-name . "KEGGgraph")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-graph" ,r-graph)
+       ("r-rcurl" ,r-rcurl)
+       ("r-xml" ,r-xml)))
+    (home-page "http://www.nextbiomotif.com") ;;no https
+    (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
+    (description
+     "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
+object as well as a collection of tools to analyze, dissect and visualize these
+graphs.  It parses the regularly updated kgml (Kegg xml) files into graph models
+maintaining all essential pathway attributes.  The package offers
+functionalities including parsing, graph operation, visualization and etc.")
+    (license license:gpl2+)))
-- 
2.29.2

Message #11 received at 45282 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <45282 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 2/2] gnu: Add r-pathview.
Date: Wed, 16 Dec 2020 23:15:33 +0100

* gnu/packages/bioconductor.scm (r-pathview): New variable.
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 36274d0b39..b4a1af4306 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9213,3 +9213,37 @@ on KEGG pathways and GO terms for major research species, including human,
 mouse, rat and budding yeast.  Mapping data between common gene IDs for budding
 yeast are also included.")
     (license license:gpl2+)))
+
+(define-public r-pathview
+  (package
+    (name "r-pathview")
+    (version "1.30.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pathview" version))
+       (sha256
+        (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
+    (properties `((upstream-name . "pathview")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-graph" ,r-graph)
+       ("r-kegggraph" ,r-kegggraph)
+       ("r-keggrest" ,r-keggrest)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-png" ,r-png)
+       ("r-rgraphviz" ,r-rgraphviz)
+       ("r-xml" ,r-xml)))
+    (home-page "https://pathview.uncc.edu/")
+    (synopsis "Tool set for pathway based data integration and visualization")
+    (description
+     "@code{r-pathview} is a tool set for pathway based data integration and
+visualization.  It maps and renders a wide variety of biological data on
+relevant pathway graphs.  All users need is to supply their data and specify
+the target pathway.  This package automatically downloads the pathway graph
+data, parses the data file, maps user data to the pathway, and render pathway
+graph with the mapped data.  In addition, @code{r-pathview} also seamlessly
+integrates with pathway and gene set (enrichment) analysis tools for
+large-scale and fully automated analysis.")
+    (license license:gpl3+)))
-- 
2.29.2

Message #16 received at 45282-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: 45282-done <at> debbugs.gnu.org
Subject: Re: [PATCH 1/2] gnu: Add r-kegggraph.
Date: Thu, 17 Dec 2020 12:32:15 +0100

I applied these with a few changes (moved the packages around and
reordered the commits).

Thanks!

-- 
Ricardo

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