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>

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--
Benjamin Datko
Systems Staff
Center for Advance Research Computing
E: bda...@carc.unm.edu

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