Question: Galaxy on Bio-Linux 8 does not start 'ExpatError'
0
gravatar for juls.jaeger
3.0 years ago by
juls.jaeger10
United Kingdom
juls.jaeger10 wrote:

Hi everyone!

I just installed Bio-Linux 8, which has Galaxy on board. 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

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by juls.jaeger10
0
gravatar for Bjoern Gruening
3.0 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

if this is a fresh installation you should contact the Biolinux people to get this fixed. For this looks like there is one corrupted or empty config file. Please check this. Especially the config/galaxy.ini file.

Cheers,

Bjoern

ADD COMMENTlink written 3.0 years ago by Bjoern Gruening5.1k
0
gravatar for juls.jaeger
3.0 years ago by
juls.jaeger10
United Kingdom
juls.jaeger10 wrote:

Hi Bjoern,

thanks for the answer. I subscribed to the Biolinux mailinglist and hope to have access tomorrow, to forward the problem to them (t.

Yes I have the same suspicion that it has something to do with the galaxy config file. There are some similar, but not identical cases out there with some ideas to fix it, but I will probably wait till I get feedback from.

By the way, Galaxy works when I run BioLinux in Virtualbox on windows.

Happy anyway for any input, please let me know if someone experienced similar problems.

Thanks, Julian

ADD COMMENTlink written 3.0 years ago by juls.jaeger10

It's running in VM on Windows, uh this is strange. Please make sure you not accidentally removed some file content during editing.

Ciao,

Bjoern 

ADD REPLYlink written 3.0 years ago by Bjoern Gruening5.1k
0
gravatar for juls.jaeger
3.0 years ago by
juls.jaeger10
United Kingdom
juls.jaeger10 wrote:

Hi, no I actually I did not edit at all, I used not the .iso file of biolinux for the VB installation. The biolinux side has a ready-to-go OVA file for use with VirtualBox/VMWare.

Thanks, J

ADD COMMENTlink written 3.0 years ago by juls.jaeger10

Ah, ok so maybe they have inconsistent builds.

ADD REPLYlink written 3.0 years ago by Bjoern Gruening5.1k
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