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 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.
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--
Bioinformatician
MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom
Edinburgh EH4 2XU, UK
Tel: +44 (0)131 332 2471 Ext. 4032
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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