GNU bug report logs - #65688
[PATCH 2/2] gnu: Add r-trackviewer.

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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#65688: closed ([PATCH 2/2] gnu: Add r-trackviewer.)
Date: Sat, 02 Sep 2023 09:58:01 +0000

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Your message dated Sat, 02 Sep 2023 11:55:55 +0200
with message-id <87h6ocdhj3.fsf <at> elephly.net>
and subject line [PATCH 2/2] gnu: Add r-trackviewer.
has caused the debbugs.gnu.org bug report #65688,
regarding [PATCH 2/2] gnu: Add r-trackviewer.
to be marked as done.

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help-debbugs <at> gnu.org.)


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65688: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=65688
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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH 2/2] gnu: Add r-trackviewer.
Date: Fri, 1 Sep 2023 20:45:12 +0000

* gnu/packages/bioconductor.scm (r-trackviewer): New variable.
---
 gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 88592c4f71..0070d7777c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9931,6 +9931,48 @@ (define-public r-tkwidgets
      "This package implements widgets to provide user interfaces.")
     (license license:artistic2.0)))
 
+(define-public r-trackviewer
+  (package
+    (name "r-trackviewer")
+    (version "1.36.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "trackViewer" version))
+              (sha256
+               (base32
+                "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))))
+    (properties `((upstream-name . "trackViewer")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi
+                             r-biocgenerics
+                             r-genomeinfodb
+                             r-genomicalignments
+                             r-genomicfeatures
+                             r-genomicranges
+                             r-graph
+                             r-grimport
+                             r-gviz
+                             r-htmlwidgets
+                             r-interactionset
+                             r-iranges
+                             r-plotrix
+                             r-rgraphviz
+                             r-rhdf5
+                             r-rsamtools
+                             r-rtracklayer
+                             r-s4vectors
+                             r-scales
+                             r-strawr))
+    (native-inputs (list esbuild r-knitr))
+    (home-page "https://bioconductor.org/packages/trackViewer")
+    (synopsis "Web interface for interactive multi-omics data analysis")
+    (description
+     "TrackViewer offers multi-omics analysis with web based  tracks and lollipops.
+Visualize mapped reads along with annotation as track layers for NGS dataset
+such as @code{ChIP-seq,} RNA-seq, @code{miRNA-seq,} DNA-seq, SNPs and
+methylation data.")
+    (license license:gpl2+)))
+
 (define-public r-transcriptr
   (package
     (name "r-transcriptr")
-- 
2.34.1

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 65688-done <at> debbugs.gnu.org
Subject: [PATCH 2/2] gnu: Add r-trackviewer.
Date: Sat, 02 Sep 2023 11:55:55 +0200

Thanks for the patch!

This one needed a little more work.  The “esbuild” in the native inputs
was added by the importer because the package includes minified
JavaScript files.

Luckily it’s just one file and we can replace it easily.  I’ve made the
necessary changes and pushed it with commit
8c0c94bf9f70a9252cd6f4261d2bce6bdba2bd0b to the “master” branch.

-- 
Ricardo

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