Question: problems with local galaxy
1
gravatar for elmujtar.veronica
3.5 years ago by
Argentina
elmujtar.veronica30 wrote:

Hello,

I installed galaxy locally and was successful in register user, become adminstrator, uploading files, install tools, create a library.  However after I shut down the program, it cannot re-start.  I entered command sh run.sh and the startup fails here:

Traceback (most recent call last):
  File "/home/vero/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 44, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/vero/galaxy-dist/lib/galaxy/app.py", line 82, in __init__
    self._configure_toolbox()
  File "/home/vero/galaxy-dist/lib/galaxy/config.py", line 702, in _configure_toolbox
    self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
  File "/home/vero/galaxy-dist/lib/galaxy/tools/__init__.py", line 143, in __init__
    self.load_integrated_tool_panel_keys()
  File "/home/vero/galaxy-dist/lib/galaxy/tools/__init__.py", line 376, in load_integrated_tool_panel_keys
    tree = parse_xml( self.integrated_tool_panel_config )
  File "/home/vero/galaxy-dist/lib/galaxy/util/__init__.py", line 174, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/vero/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/vero/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 583, in parse
    parser.feed(data)
  File "/home/vero/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 1242, in feed
    self._parser.Parse(data, 0)
ExpatError: not well-formed (invalid token): line 117, column 38

 

I only install python-dev because i need it for install cutadapt dependencies. And I only modify the galaxy.ini to set email for the administrator and to set the directory for tool dependencies.

 

Thank you for your help in starting galaxy again

Veronica

 

 

 

software error galaxy • 900 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by elmujtar.veronica30
1
gravatar for Dannon Baker
3.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

It looks like the integrated_tool_panel got mangled somehow.

This file can be automatically regenerated, so the easiest thing to do would be to rename it temporarily and see if that fixes your issue. So, something like 'mv config/integrated_tool_panel.xml config/integrated_tool_panel.xml.backup'.

If that doesn't fix the problem, it'd be worth looking inside the file at the specified line and column to see what might be going on.

ADD COMMENTlink written 3.5 years ago by Dannon Baker3.7k
0
gravatar for elmujtar.veronica
3.5 years ago by
Argentina
elmujtar.veronica30 wrote:

thanks, it is working now. But if I shut down the program, I found the same error and it cannot re-start again.

Veronica

ADD COMMENTlink written 3.5 years ago by elmujtar.veronica30

Well that's interesting.  Can you look inside the file (or feel free to just email it to me or attach it here) and see what's going on at that character indication?

ADD REPLYlink written 3.5 years ago by Dannon Baker3.7k
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