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.