Hi all, we are testing a newly cloned galaxy. Which was running as expected a few hours ago. After some modification to galaxy.yml file we got this error message but after using the original galaxy.yml version it still does not run. Regenerating static plugin directories. Activating virtualenv at .venv Traceback (most recent call last): File "./scripts/manage_tool_dependencies.py", line 60, in <module> main() File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in main action_func(args, kwargs) File "./scripts/manage_tool_dependencies.py", line 20, in _init_if_needed _build_dependency_manager_no_config(kwargs) File "./scripts/manage_tool_dependencies.py", line 48, in _build_dependency_manager_no_config dependency_manager = DependencyManager(**dependency_manager_kwds) File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line 77, in __init__ self.dependency_resolvers = self.__build_dependency_resolvers(conf_file) File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line 241, in __build_dependency_resolvers plugin_source = plugin_config.plugin_source_from_path(conf_file) File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ", line 78, in plugin_source_from_path return ('xml', ElementTree.parse(path).getroot()) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse tree.parse(source, parser) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse parser.feed(data) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed self._raiseerror(v) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err xml.etree.ElementTree.ParseError: junk after document element: line 54, column 0 Cheers Jochen