[Bio-Linux] FW: Galaxy on Bio-Linux 8 does not start. 'ExpatError'

[Tim Booth]

Hi Julian,

I've not seen this error before.  It looks like it is trying to load one
of the tool configuration files and the file is either missing or empty,
so it seems there is a problem with the installation.

Galaxy should run automatically and I've tested this on a fresh
Bio-Linux 8 installation.  To manually control it you can run "sudo stop
galaxy" or "sudo start galaxy" but other ways of running the server
might not work.

To see if files are missing please run:

sudo -u Debian-galaxy ls -l /usr/lib/galaxy-server --color=auto

Does anything show up in red?  Can you please post the listing you get?

Cheers,

TIM


On Wed, 2015-07-15 at 10:41 +0100, jaeger.julian at gmx.net wrote:
> Hi everyone!
> 
> I just installed Bio-Linux 8. Unfortunatly Galaxy won't start.
> 
> Here is the recent traceback from the logfile:
> 
> Traceback (most recent call last):
>   File "/usr/lib/galaxy-server/lib/galaxy/webapps/galaxy/buildapp.py",
> line 39, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/usr/lib/galaxy-server/lib/galaxy/app.py", line 63, in
> __init__
>     self._configure_tool_data_tables( from_shed_config=False )
>   File "/usr/lib/galaxy-server/lib/galaxy/config.py", line 592, in
> _configure_tool_data_tables
>     from_shed_config=from_shed_config )
>   File "/usr/lib/galaxy-server/lib/galaxy/tools/data/__init__.py",
> line 63, in load_from_config_file
>     tree = util.parse_xml( filename )
>   File "/usr/lib/galaxy-server/lib/galaxy/util/__init__.py", line 154,
> in parse_xml
>     tree = ElementTree.parse(fname)
>   File
> "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
>     tree.parse(source, parser)
>   File
> "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 584, in parse
>     self._root = parser.close()
>   File
> "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 1251, in close
>     self._parser.Parse("", 1) # end of data
> ExpatError: no element found: line 1, column 0
> 
>  
> 
> Can anyone help, please?
> 
>  
> 
> Many thanks , Julian
> 
>  
> 
> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
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Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
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