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