Re: [galaxy-dev] conda management of tools dependent on python3

[Björn Grüning]

Hi,

can you check the package? The package should have a dependency on
python3, if not the package seems to be broken :(

Ciao,
Bjoern

Am 03.11.2016 um 21:32 schrieb Wolfgang Maier:
> Hi Björn,
> 
> Hmm, I guess I should have phrased my question more clearly. What I'm
> trying to do is to get Galaxy to satisfy a missing tool dependency at
> *tool runtime* using a bioconda package that is only available for
> Python3. I am able to satisfy the dependency *manually* by running:
> 
> conda create --name __@
> == 
> (following the example at
> https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed),
> but when I let *Galaxy autoinstall* the package it will use python2.7
> for the environment, then fail with:
> 
> Error: Unsatisfiable package specifications.
> 
> and a hint that  conflicts with python 2.7. So my question is:
> is there any way to inform Galaxy that the dependency requires a conda
> environment based on python3?
> 
> Best,
> Wolfgang
> 
> 
> On 28.10.2016 19:14, Björn Grüning wrote:
>> Hi Wolfgang,
>>
>> can you describe step by step what you are trying to do?
>>
>> A conda package ships it's own python version, you can see this in the
>> build-string py35_0 for example. So conda can handle all python version
>> independent of the python version of miniconda.
>>
>> Cheers,
>> Bjoern
>>
>>> Dear all,
>>>
>>> I'm still pretty new to conda tool dependencies management and there is
>>> one thing I cannot find documented anywhere:
>>> How can I let conda manage tool dependencies that involve python3?
>>> If I let Galaxy install conda for me, it creates an environment with
>>> python2, then if there is a tool dependency that has a conda package
>>> built for only python3 I'm getting an error because of a conflict
>>> between that package and python2 (not surprisingly), but AFAIU conda
>>> environments are bound to one particular version of python (or is that
>>> incorrect?).
>>>
>>> Thanks for any help with this and best wishes,
>>> Wolfgang
>>> ___
>>> 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/

Re: [galaxy-dev] conda management of tools dependent on python3

[Wolfgang Maier]

Hi Björn,

Hmm, I guess I should have phrased my question more clearly. What I'm 
trying to do is to get Galaxy to satisfy a missing tool dependency at 
*tool runtime* using a bioconda package that is only available for 
Python3. I am able to satisfy the dependency *manually* by running:


conda create --name __@ 
==

(following the example at 
https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), 
but when I let *Galaxy autoinstall* the package it will use python2.7 
for the environment, then fail with:


Error: Unsatisfiable package specifications.

and a hint that  conflicts with python 2.7. So my question is: 
is there any way to inform Galaxy that the dependency requires a conda 
environment based on python3?


Best,
Wolfgang


On 28.10.2016 19:14, Björn Grüning wrote:

Hi Wolfgang,

can you describe step by step what you are trying to do?

A conda package ships it's own python version, you can see this in the
build-string py35_0 for example. So conda can handle all python version
independent of the python version of miniconda.

Cheers,
Bjoern


Dear all,

I'm still pretty new to conda tool dependencies management and there is
one thing I cannot find documented anywhere:
How can I let conda manage tool dependencies that involve python3?
If I let Galaxy install conda for me, it creates an environment with
python2, then if there is a tool dependency that has a conda package
built for only python3 I'm getting an error because of a conflict
between that package and python2 (not surprisingly), but AFAIU conda
environments are bound to one particular version of python (or is that
incorrect?).

Thanks for any help with this and best wishes,
Wolfgang
___
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/

Re: [galaxy-dev] galaxy - velvet devteam revision 08256557922f

[Fernandez Edgar]

Hey everyone,

I haven’t got a feedback from you.
If you have any suggestions, I’m a little bit confused with this problem.

Thank you very much!

Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
•  Bur. : 1-514-343-6111 poste 16568


From: Fernandez Edgar
Sent: October-31-16 11:40 AM
To: galaxy-...@bx.psu.edu
Subject: [galaxy-dev] galaxy - velvet devteam revision 08256557922f

Hey Guys,

I need your help understanding what’s happening with velvet  devteam revision 
08256557922f.

After installing it, velvet was giving me the following error:
galaxy.jobs.handler WARNING 2016-10-20 12:15:11,986 (1599) Tool 
'toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0' removed from 
tool config, unable to run job galaxy.jobs.handler ERROR 2016-10-20 
12:15:12,165 (1599) Error checking job readiness
galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job 
readiness

I realized velvet needed that galaxy was restarted.

Now, velvet finishes his jobs (becomes green) however, the following message is 
on galaxy’s
Job output not returned from cluster

And you can see in the logs of the handler:
galaxy.jobs DEBUG 2016-10-31 10:17:08,548 (1669) Working directory for job is: 
/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669
galaxy.jobs.handler DEBUG 2016-10-31 10:17:08,567 (1669) Dispatching to drmaa 
runner
galaxy.jobs DEBUG 2016-10-31 10:17:08,621 (1669) Persisting job destination 
(destination id: torque)
galaxy.jobs.runners DEBUG 2016-10-31 10:17:08,630 Job [1669] queued (63.397 ms)
galaxy.jobs.handler INFO 2016-10-31 10:17:08,652 (1669) Job dispatched
galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Building dependency shell 
command for dependency 'velvet'
galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Find dependency velvet version 
1.2.10
galaxy.tools.deps DEBUG 2016-10-31 10:17:08,896 Resolver tool_shed_packages 
returned  (isnull? False)
galaxy.jobs.command_factory INFO 2016-10-31 10:17:08,945 Built script 
[/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh] for 
tool 
command[PACKAGE_BASE=/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f;
 export PACKAGE_BASE; . 
/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f/env.sh;
 velveth 2>&1 | grep "Version" | sed -e 's/Version //' > 
/home/galaxy/galaxy-prod/database/tmp/GALAXY_VERSION_STRING_1669 2>&1; python 
/home/galaxy/galaxy-prod/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/velvet/08256557922f/velvet/velveth_wrapper.py
 '/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat' 
'/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/dataset_4306_files' 
21  -fasta -short /home/galaxy/galaxy-prod/database/files/003/dataset_3537.dat]
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Building dependency shell 
command for dependency 'samtools'
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Find dependency samtools 
version None
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver tool_shed_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned 
 (isnull? 
True)
galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned 
 (isnull? 
True)
galaxy.tools.deps WARNING 2016-10-31 10:17:09,145 Failed to resolve dependency 
on 'samtools', ignoring
galaxy.jobs.runners DEBUG 2016-10-31 10:17:09,153 (1669) command is: mkdir -p 
working; cd working; 
/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh; 
return_code=$?; cd 
'/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669'; python 
"/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/set_metadata_KQTExg.py"
 "/home/galaxy/galaxy-prod/database/tmp/tmpLU0HQy" 
"/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/working/galaxy.json"
 
"/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_in_HistoryDatasetAssociation_4437_kIYXWa,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_kwds_HistoryDatasetAssociation_4437_ArCXyb,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_out_HistoryDatasetAssociation_4437_l28qWr,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_results_HistoryDatasetAssociation_4437_oTDjOd,/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_override_HistoryDatasetAssociation_4437_8VzdJw"
 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,202 (1669) submitting file 

Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

[Yip, Miu ki]

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

Thank you!

> On Nov 3, 2016, at 12:59 PM, Peter Cock  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  wrote:
>> Hi Peter,
>> 
>> Line 44 is oddly specific. Nevertheless, we have this as the 44th line in 
>> the xml file.
>> 
>> > version="" />
>> 
>> This tool is not the one trying to be installed.
>> 
>> Thanks,
>> Miuki
>> On Nov 3, 2016, at 10:28 AM, Peter Cock 
>> > 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  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 
>>   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:
  

Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

[Peter Cock]

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  wrote:
> Hi Peter,
>
> Line 44 is oddly specific. Nevertheless, we have this as the 44th line in the 
> xml file.
>
>  version="" />
>
> This tool is not the one trying to be installed.
>
> Thanks,
> Miuki
> On Nov 3, 2016, at 10:28 AM, Peter Cock 
> > 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  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 
>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/

[galaxy-dev] purge dataset at a different location

[Mark Xiao]

Dear Galaxy Developers,

Because of specific use case, our transfer tool need to keep the datasets
in a different location instead of the default location, so we'd like to
purge datasets according to its "external_filename" (we found this column
in the dataset table in the database). Is there a way or some code to
modify so that when we try to purge a dataset or a history in Galaxy, the
file located at a dataset's external_filename can also be deleted?

Thanks in advance,
Mark Xiao
___
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/

Re: [galaxy-dev] 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  
> 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 
>> 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/

Re: [galaxy-dev] 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  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 
> 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/

Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

[Marius van den Beek]

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 
 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/

[galaxy-dev] 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 
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/