--- a/jbrowse.xml	Wed Sep 11 09:40:36 2019 -0400
+++ b/jbrowse.xml	Wed Dec 18 10:46:52 2019 -0500
@@ -16,6 +16,8 @@
 ## but nice if users want to reproduce locally
 cp $trackxml $output.files_path/galaxy.xml &&
 
+export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse  &&
+
 ## Once that's done, we run the python script to handle the real work
 python '$__tool_directory__/jbrowse.py'
 
@@ -28,14 +30,14 @@
 $trackxml &&
 
 #if str($standalone) == "Complete":
-    mv $output.files_path/index.html $output;
+    cp $output.files_path/index.html $output;
 #else:
-    mv $dummyIndex $output;
+    cp $dummyIndex $output;
 #end if
 
 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
 #if str($uglyTestingHack) == "enabled":
-    mv $trackxml $output
+    cp $trackxml $output
 #end if
   ]]></command>
   <configfiles>