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>
File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in main
File "./scripts/manage_tool_dependencies.py", line 20, in _init_if_needed
File "./scripts/manage_tool_dependencies.py", line 48, in
dependency_manager = DependencyManager(**dependency_manager_kwds)
File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line 77,
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,
return ('xml', ElementTree.parse(path).getroot())
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
xml.etree.ElementTree.ParseError: junk after document element: line 54,
The May 2019 Galactic News is here! See
https://galaxyproject.org/news/2019-05-galaxy-update/ for details
- **Early registration ends 17 May**
- Poster and Demo Abstract Submission is open
- Travel Fellowships: 2nd round ends this Friday
- GigaScience returns as a GCC sponsor!
- GTN CoFest and Community Call: 16 May
- Plus 17 other upcoming events in the next 90 days
- 265 new publications, great resources lead to great insight.
- Some most excellent Galaxy Platform News, including a single cell 'omics
workbench, network analysis, subcellular spatial organization modeling, and
- A new entry to The Galactic Blog, Galaxy hearts GCP.
- At least 11 Open positions in six countries on two continents.
- Updates to training materials.
- New releases.
See you in two months in Freiburg,
Dave C, Mo, and the Galaxy Community