Awesome! After changing β€œ&” to β€œand”, it worked!

Thank you!

> On Nov 3, 2016, at 12:59 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 
> Good news - this is the bug I though it was, the ampersand
> should be escaped as &amp; 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
>> ___________________________________________________________
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