diff jbrowse2/jbrowse2.xml @ 10:0db895a99532 draft default tip

Uploaded

--- a/jbrowse2/jbrowse2.xml	Fri Jan 05 05:06:21 2024 +0000
+++ b/jbrowse2/jbrowse2.xml	Fri Jan 05 22:26:16 2024 +0000
@@ -14,16 +14,12 @@
 ## Copy the XML file into the directory, mostly for debugging
 ## but nice if users want to reproduce locally
 cp '$trackxml' '$output.files_path/galaxy.xml' &&
-
-export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&
-
+export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse)) &&
 ## Once that's done, we run the python script to handle the real work
 python '$__tool_directory__/jbrowse2.py'
-
 --jbrowse \${JBROWSE_SOURCE_DIR}
-
 --outdir '$output.files_path'
-'$trackxml' &&
+--xml '$trackxml' &&
 
 cp '$output.files_path/index.html' '$output'