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

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 65688 in the body.
You can then email your comments to 65688 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

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

Message #10 received at 65688-done <at> debbugs.gnu.org (full text, mbox):

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

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.