Mercurial > repos > iuc > jbrowse

diff jbrowse-fromdir.xml @ 35:3235aeb45c22 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
author iuc
date Wed, 18 Dec 2019 10:46:52 -0500
parents 1cfc579079a6
children 8774b28235bb
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--- a/jbrowse-fromdir.xml	Wed Sep 11 09:40:36 2019 -0400
+++ b/jbrowse-fromdir.xml	Wed Dec 18 10:46:52 2019 -0500
@@ -7,12 +7,15 @@
   <command detect_errors="exit_code"><![CDATA[
 ## Create output directory
 mkdir -p $output.files_path &&
+
+export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse  &&
+
 ## Copy in jbrowse
 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
 
 ## Copy in data directory
 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
-mv $output.files_path/index.html $output
+cp $output.files_path/index.html $output
 ]]></command>
   <inputs>
     <param label="JBrowse Data Directory"