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
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