Mercurial > repos > fubar > jbrowse2

diff autogenJB2.xml @ 39:bc57164eb270 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
author fubar
date Fri, 01 Mar 2024 01:03:09 +0000
parents 5f39f745682f
children e1a3d3221ed3
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line diff
--- a/autogenJB2.xml	Fri Mar 01 00:40:38 2024 +0000
+++ b/autogenJB2.xml	Fri Mar 01 01:03:09 2024 +0000
@@ -10,6 +10,7 @@
     <expand macro="requirements"/>
     <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&
 python '$__tool_directory__/autogenJB2.py'
 #for $key in $autoCollection.keys():
     #if $autoCollection[$key].ext == 'fasta':
@@ -23,6 +24,7 @@
     #end if
 #end for
 --outdir '$output.files_path'
+--jbrowse2path \${JBROWSE2_PATH}
 --sessName "Autogen JBrowse" &&
 
   cp '$output.files_path/index.html' '$output'