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.b...@usys.ethz.ch > <mailto:jochen.b...@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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > %(web_page_url)s > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > -- 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.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
