Hej Nate, thx for your email. We did not touch that file. Maybe we just have a corrupted yml file? Is there a good way to check (lint) that file? Cheers Jochen On 09.05.19 19:56, Nate Coraor wrote:

Hi Jochen,

Could you check the value of the 'dependency_resolvers_config_file' option and verify that the file it points at (by default, config/dependency_resolvers_conf.xml) is properly formatted?

--nate

On Thu, May 9, 2019 at 1:25 PM Jochen Bick <jochen.bick@usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch>> wrote:

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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-- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick@usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch