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.
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