I think you may have hit the same bug I found recently:

https://github.com/galaxyproject/galaxy/issues/3084

What is line 44 of your integrated_tool_panel.xml file?

Peter

On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki <m...@cshl.edu> wrote:
> Hi all,
>
> While trying to install tools from the toolshed via the browser interface, an 
> error keeps appearing and nothing is abled to be installed. Currently using 
> the latest version of Galaxy and having tried to install several different 
> tools, the following error keeps appearing in the log file.
>
> galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload on 
> 'main'
> Exception in thread Thread-2:
> Traceback (most recent call last):
>   File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner
>     self.run()
>   File "/usr/lib64/python2.7/threading.py", line 764, in run
>     self.__target(*self.__args, **self.__kwargs)
>   File 
> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 
> 147, in on_any_event
>     self._handle(event)
>   File 
> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 
> 150, in _handle
>     self.reload_callback()
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", 
> line 78, in <lambda>
>     self._tool_conf_watcher = get_tool_conf_watcher( lambda: 
> reload_toolbox(app))
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line 
> 56, in reload_toolbox
>     app.toolbox = _get_new_toolbox(app)
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line 
> 72, in _get_new_toolbox
>     new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, 
> app.toolbox._tool_conf_watcher)
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", line 
> 110, in __init__
>     tool_conf_watcher=tool_conf_watcher
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", 
> line 1037, in __init__
>     super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, 
> app, tool_conf_watcher=tool_conf_watcher)
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", 
> line 69, in __init__
>     self._init_integrated_tool_panel( app.config )
>   File 
> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py",
>  line 36, in _init_integrated_tool_panel
>     self._load_integrated_tool_panel_keys()
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", 
> line 368, in _load_integrated_tool_panel_keys
>     tree = parse_xml( self._integrated_tool_panel_config )
>   File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line 
> 211, in parse_xml
>     root = tree.parse( fname, parser=ElementTree.XMLParser( 
> target=DoctypeSafeCallbackTarget() ) )
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse
>     parser.feed(data)
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed
>     self._raiseerror(v)
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in 
> _raiseerror
>     raise err
> ParseError: not well-formed (invalid token): line 44, column 71
>
> Is there an XML or configuration file which needs to be changed for this to 
> work? Not sure how to proceed.
>
> Thanks!
> Miuki
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