Hi Graeme, It looks like your integrated_tool_panel.xml file has been corrupted. You can move/remove this file and it will be recreated the next time Galaxy is started up.
Thanks for using Galaxy, Dan On Sep 3, 2014, at 3:54 AM, Graeme Grimes <graeme.gri...@igmm.ed.ac.uk> wrote: > I have tried to restart Galaxy after restoring my database from a backup. > > Here is the error message I get in the log file. Any idea what is wrong and > how to fix this problem? > > ------------------------------ > galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Loading job configuration from > /export/users/galaxy/galaxy-test/universe_wsgi.ini > galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Done loading job configuration > Traceback (most recent call last): > File > "/export/users/galaxy/galaxy-test/lib/galaxy/webapps/galaxy/buildapp.py", > line 35, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File "/export/users/galaxy/galaxy-test/lib/galaxy/app.py", line 102, in > __init__ > self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) > File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py", line > 118, in __init__ > self.load_integrated_tool_panel_keys() > File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py", line > 283, in load_integrated_tool_panel_keys > tree = parse_xml( self.integrated_tool_panel_config ) > File "/export/users/galaxy/galaxy-test/lib/galaxy/util/__init__.py", line > 132, in parse_xml > tree = ElementTree.parse(fname) > File > "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 859, in parse > tree.parse(source, parser) > File > "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 583, in parse > parser.feed(data) > File > "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 1242, in feed > self._parser.Parse(data, 0) > ExpatError: not well-formed (invalid token): line 117, column 1 > Removing PID file /var/run/paster.pid > ----------------- > > > Thanks, > > Graeme > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
