Trying a run with an older value of the helm chart (3.4.2) and cvmfs disabled I get some hard coded CVMFS requirements that make the process fail:
No handlers could be found for logger "__main__" Traceback (most recent call last): File "/galaxy/server/scripts/galaxy-main", line 299, in <module> main() File "/galaxy/server/scripts/galaxy-main", line 295, in main app_loop(args, log) File "/galaxy/server/scripts/galaxy-main", line 142, in app_loop attach_to_pools=args.attach_to_pool, File "/galaxy/server/scripts/galaxy-main", line 108, in load_galaxy_app **kwds File "/galaxy/server/lib/galaxy/app.py", line 115, in __init__ self._configure_tool_data_tables(from_shed_config=False) File "/galaxy/server/lib/galaxy/config/__init__.py", line 1077, in _configure_tool_data_tables config_filename=self.config.tool_data_table_config_path) File "/galaxy/server/lib/galaxy/tools/data/__init__.py", line 80, in __init__ self.load_from_config_file(single_config_filename, self.tool_data_path, from_shed_config=False) File "/galaxy/server/lib/galaxy/tools/data/__init__.py", line 117, in load_from_config_file tree = util.parse_xml(filename) File "/galaxy/server/lib/galaxy/util/__init__.py", line 236, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/cvmfs/main.galaxyproject.org/config/shed_tool_data_table_conf.xml'
This is against a fixed container tag for that particular timepoint of the helm chart. So we should check that CVMFS disabled is actually not letting slip any env vars or so on...
galaxy.yml: ---- galaxy: admin_users: email@example.com,firstname.lastname@example.org build_sites_config_file: /galaxy/server/config/build_sites.yml builds_file_path: '/cvmfs/data.galaxyproject.org/managed/location/builds.txt'
Exception: Problem parsing the XML in file /galaxy/server/config/job_conf.xml, please correct the indicated portion of the file and restart Galaxy. '>=' not supported between instances of 'NoneType' and ‘tuple’
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