Following the directions from here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I'm trying to get pbs_python to work as I'm using torque for scheduling galaxy jobs.  

Note: This is a fresh install of galaxy from galaxy-dist on CentOS 5.10

I have pbs_python 4.4.0 module installed into a source-built version of python/2.7.6

I get the following error in the output of run.sh:

galaxy.jobs INFO 2014-03-03 15:46:45,485 Handler 'main' will load all configured runner plugins
Traceback (most recent call last):
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/app.py", line 130, in __init__
    self.job_manager = manager.JobManager( self )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/manager.py", line 31, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/handler.py", line 30, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/handler.py", line 568, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/__init__.py", line 449, in get_job_runner_plugins
    module = __import__( module_name )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/runners/pbs.py", line 31, in <module>
    raise Exception( egg_message % str( e ) )
Exception:

The 'pbs' runner depends on 'pbs_python' which is not installed or not
configured properly.  Galaxy's "scramble" system should make this installation
simple, please follow the instructions found at:

    http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

Additional errors may follow:
pbs-python==4.3.5

This is the job_conf.xml file:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
    </plugins>
    <handlers>
        <handler id="dirigo"/>
    </handlers>
    <destinations default="pbs_default">
        <destination id="pbs_default" runner="pbs"/>
                <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=4</param>
    </destinations>
</job_conf>

I did not use the scramble system to install the pbs_python module.  I downloaded the latest version
available and installed it from the root account.


--
Pete Schmitt


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