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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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