Hi Marius, Thanks for the reply!
I have tried moving the file and just deleting the file all together. I am still running into this error. Thanks, Miuki > On Nov 3, 2016, at 10:29 AM, Marius van den Beek <m.vandenb...@gmail.com> > wrote: > > 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 >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
