That is really odd - there is some problem parsing the job_conf.xml
file but the exception shown there doesn't seem to match the contents
you previously posted. Did you make modifications after you pasted
that?

It might be easier to winnow down the error if you explicitly set a a
default handler in your <handlers> definition - so use <handlers
default="main">.

-John

On Tue, Jul 28, 2015 at 4:31 PM, Benjamin Datko <bda...@carc.unm.edu> wrote:
> Hello John,
>
>> Do you have a single process Galaxy setup (i.e. is [server:main] the only
>> server:* section in your galaxy.ini file?
>
> Yes I only have a single process setup within my galaxy.ini file. The HTTP
> server configuration from my galaxy.ini file can be seen below:
>
> # ---- HTTP Server
> ----------------------------------------------------------
>
> # Configuration of the internal HTTP server.
>
> [server:main]
>
> # The internal HTTP server to use.  Currently only Paste is provided.  This
> # option is required.
> use = egg:Paste#http
>
> # The port on which to listen.
> port = 1111
>
> # The address on which to listen.  By default, only listen to localhost
> (Galaxy
> # will not be accessible over the network).  Use '0.0.0.0' to listen on all
> # available network interfaces.
> host = 0.0.0.0
>
> # Use a threadpool for the web server instead of creating a thread for each
> # request.
> use_threadpool = True
>
> # Number of threads in the web server thread pool.
> #threadpool_workers = 10
>
> # Set the number of seconds a thread can work before you should kill it
> # (assuming it will never finish) to 3 hours.  Default is 600 (10 minutes).
> threadpool_kill_thread_limit = 10800
>
> So I have noticed when I tried to upload a "test.fasta" file for job
> submission the file fails to upload seen in the history with "This jobs is
> waiting to run". I am also unable to view the data file as well. Since I am
> failing to upload a data set I cannot actualy test any job submission. While
> server is running and I attempted to upload the file I noticed the output
> shown below:
>
>  File "/users/galaxy/galaxy/lib/galaxy/jobs/runners/pbs.py", line 302, in
> queue_job
>     fh = file(job_file, "w")
> IOError: [Errno 2] No such file or directory:
> '/users/galaxy/galaxy/database/pbs/21.sh'
>
> Below is the last few lines of my paster.log:
>
> galaxy.tools.data WARNING 2015-07-22 09:53:53,726 Line 1 in tool data table
> 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to
> separate fields):
> <Server-Side Genome List>
> galaxy.tools.data DEBUG 2015-07-22 09:53:53,731 Loaded tool data table
> 'igv_broad_genomes'
> galaxy.jobs DEBUG 2015-07-22 09:53:53,910 Loading job configuration from
> ./config/job_conf.xml
> galaxy.jobs ERROR 2015-07-22 09:53:53,910 Problem parsing the XML in file
> /users/galaxy/galaxy/config/job_conf.xml, please correct the indicated
> portion of the file and restart Galaxy.'NoneType' object has no attribute
> 'get'
> Traceback (most recent call last):
>   File "/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 133, in
> __init__
>     self.__parse_job_conf_xml(tree)
>   File "/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 195, in
> __parse_job_conf_xml
>     self.default_handler_id = self.__get_default(handlers,
> self.handlers.keys())
>   File "/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 411, in
> __get_default
>     rval = parent.get('default')
> AttributeError: 'NoneType' object has no attribute 'get'
> Traceback (most recent call last):
>   File "/users/galaxy/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
> 51, in app_factory
>     app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs
> )
>   File "/users/galaxy/galaxy/lib/galaxy/app.py", line 85, in __init__
>     self.job_config = jobs.JobConfiguration(self)
>   File "/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 140, in
> __init__
>     raise config_exception(e, job_config_file)
> Exception: Problem parsing the XML in file
> /users/galaxy/galaxy/config/job_conf.xml, please correct the indicated
> portion of the file and restart Galaxy.'NoneType' object has no attribute
> 'get'
> Removing PID file paster.pid
>
> BenD
>
> On 7/27/2015 7:13 AM, John Chilton wrote:
>>
>> This pretty much looks like it should work to me. Do you have a single
>> process Galaxy setup (i.e. is [server:main] the only server:* section
>> in your galaxy.ini file? Is there anything in the Galaxy log that
>> indicates a problem (can you send me a portion of log or post it here
>> related to the job submission)?.
>>
>> -John
>>
>> On Wed, Jul 22, 2015 at 7:51 PM, Benjamin Datko <bda...@carc.unm.edu>
>> wrote:
>>>
>>> Hello all,
>>>
>>> I am trying to config a cluster galaxy server using PBS torque. I have
>>> gone
>>> through the documentation but it is not clear to me how the job_conf.xml
>>> should be set up. Are there detailed documents on how galaxy works with
>>> the
>>> resource manger and how galaxy submits jobs?
>>>
>>> My current problem jobs can be created and submitted but within the
>>> history
>>> tab I have "this job is waiting to run". The job never gets submitted to
>>> PBS
>>> torque queue and cannot be seen using qstat. My job_conf.xml is shown
>>> below.
>>> If anyone can give a sample to a working configuration file for
>>> job_conf.xml
>>> using PBS torque that will be most appreciated.
>>>
>>> Ben
>>>
>>> <?xml version="1.0"?>
>>> <!-- A sample job config that explicitly configures job running the way
>>> it
>>> is configured by default (if there is no explicit config). -->
>>> <job_conf>
>>> <plugins>
>>>      <plugin id="pbs" type="runner"
>>> load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
>>> </plugins>
>>> <handlers>
>>>      <handler id="main"/>
>>> </handlers>
>>> <destinations default="Core2">
>>>      <destination id="Core2" runner="pbs">
>>>          <param id="Resource_List">-l
>>> walltime=24:00:00,nodes=1:ppn=2</param>
>>>      </destination>
>>> </destinations>
>>> </job_conf>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
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>
>
> --
> Benjamin Datko
> Systems Staff
> Center for Advance Research Computing
> E: bda...@carc.unm.edu
>
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