Thanks this fixed the problem. Graeme On 03/09/2014 18:30, Daniel Blankenberg wrote:

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.Grimes@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

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