Awesome! After changing “&” to “and”, it worked! Thank you!

On Nov 3, 2016, at 12:59 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Good news - this is the bug I though it was, the ampersand should be escaped as & in the XML file:

https://github.com/galaxyproject/galaxy/issues/3084

More good news: This will likely be fixed in the next release of Galaxy:

https://github.com/galaxyproject/galaxy/pull/3122

Right now I suggest you manually edit these XML files to use the word "and" instead of "&".

Peter

On Thu, Nov 3, 2016 at 2:36 PM, Yip, Miu ki <myip@cshl.edu> wrote:

...

Hi Peter,

Line 44 is oddly specific. Nevertheless, we have this as the 44th line in the xml file.

<label id="cshl_rnaseq_proc_qc" text="Post-Mapping Processing & QC" version="" />

This tool is not the one trying to be installed.

Thanks, Miuki On Nov 3, 2016, at 10:28 AM, Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote:

I think you may have hit the same bug I found recently:

https://github.com/galaxyproject/galaxy/issues/3084

What is line 44 of your integrated_tool_panel.xml file?

Peter

On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki <myip@cshl.edu> 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/

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