It looks like your integrated_tool_panel.xml file has been corrupted somehow.
You can move this file to a backup location (or delete) and it should be
automatically regenerated on Galaxy startup. If this fixes the issue, could you
share a copy of the file? It might be helpful for us to try to figure out what
happened to it.
Thanks for using Galaxy,
On Nov 14, 2012, at 4:25 AM, Joachim Jacob wrote:
> Hi Jeremy,
> Thanks for you assistance. I would love to try your suggestions, but Galaxy
> won't start anymore.
> I have found the root cause of the problems: my home partition has become too
> small, due to a fat 'job_working_directory'. I didn't expect it to become so
> big (especially with tophat output). Now I have the job_working_directory
> mounted on our network share. So I restart Galaxy, and got this error:
> Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
> 36, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 85, in __init__
> self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 84, in
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 236, in
> tree = util.parse_xml( self.integrated_tool_panel_config )
> File "/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in
> tree = ElementTree.parse(fname)
> line 859, in parse
> tree.parse(source, parser)
> line 584, in parse
> self._root = parser.close()
> line 1251, in close
> self._parser.Parse("", 1) # end of data
> ExpatError: unclosed token: line 109, column 4
> Removing PID file main.pid
> Before dragging up my backup, any idea how to fix this otherwise? I suspect
> that mercurial could not pull all changes in, is that possible?
> On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote:
>>> One dataset I want to view in Trackster has an error
>>> ConverterDependencyException: 'A dependency (bgzip) was in an error state.
>> I've seen this once or twice before but haven't been able to track down the
>> issue yet.
>> Here are two workaround that may help you out:
>> (1) Add the dataset to a new/saved visualization and then click 'try again'
>> to try reindexing the dataset;
>> (2) copy the dataset using History Options --> Copy Datasets, then delete
>> the failing dataset and try indexing the new dataset.
>> If the dataset continues to fail, please make it available to me and I'll
>> take a look.
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