Hi Joachim,

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,

Dan


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 
> __init__
>   self.load_integrated_tool_panel_keys()
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 236, in 
> load_integrated_tool_panel_keys
>   tree = util.parse_xml( self.integrated_tool_panel_config )
> File "/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in 
> parse_xml
>   tree = ElementTree.parse(fname)
> File 
> "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 859, in parse
>   tree.parse(source, parser)
> File 
> "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 584, in parse
>   self._root = parser.close()
> File 
> "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  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?
> 
> 
> Cheers,
> Joachim
> 
> 
> 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.
>> 
>> Best,
>> J.
>> 
> ___________________________________________________________
> 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/


___________________________________________________________
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/

Reply via email to