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Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

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Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

Yip, Miu ki
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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Re: Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

Peter Cock
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 <[hidden email]> 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/
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Re: Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

Marius van den Beek
In reply to this post by Yip, Miu ki
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/

___________________________________________________________
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/
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Re: Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

Yip, Miu ki
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 <[hidden email]> 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/
>

___________________________________________________________
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/
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Re: Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

Peter Cock
In reply to this post by Peter Cock
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 <[hidden email]> 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 <[hidden email]<mailto:[hidden email]>> 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 <[hidden email]> 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/
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Re: Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

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

Thank you!

> On Nov 3, 2016, at 12:59 PM, Peter Cock <[hidden email]> 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 <[hidden email]> 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 <[hidden email]<mailto:[hidden email]>> 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 <[hidden email]> 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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