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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