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.vandenbeek@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/