galaxy-dev May 2019

galaxy-dev@lists.galaxyproject.org

18 participants
12 discussions

galaxy not running after galaxy.yml changes
by Jochen Bick 10 May '19

10 May '19

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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May Galaxy News: GCC2019 early reg, GTN CoFest, new pubs, platforms, jobs,...
by Dave Clements 06 May '19

06 May '19

Hello all, The May 2019 Galactic News is here! See https://galaxyproject.org/news/2019-05-galaxy-update/ for details - Events - GCC2019: - **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 more! - 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 -- https://galaxyproject.org/gcc2019/ https://galaxyproject.org/ https://usegalaxy.org/

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galaxy-dev May 2019