Hello Miuki,

this looks like your integrated_tool_panel.xml file has some problems.
Can you try to move this file to a different location and try the installation again?
It should be located in your galaxy directory.

Best,
Marius


On 11/03/2016 03:16 PM, Yip, Miu ki 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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