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.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


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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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