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 <m...@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.c...@googlemail.com<mailto:p.j.a.c...@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 <m...@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/
>
> 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/

Reply via email to