Hi guys, after the upgrade to v16.01 I'm getting an error related to
pbs-python when starting the job runners (the web runners seem fine).
Here's the relevant part of the log file:
galaxy.jobs.manager DEBUG 2016-05-10 15:52:49,972 Starting job handler
galaxy.jobs INFO 2016-05-10 15:52:49,972 Handler 'job0' will load all
configured runner plugins
Traceback (most recent call last):
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 63, in paste_app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf,
**kwargs )
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/app.py",
line 150, in __init__
self.job_manager = manager.JobManager( self )
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/jobs/manager.py",
line 23, in __init__
self.job_handler = handler.JobHandler( app )
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/jobs/handler.py",
line 32, in __init__
self.dispatcher = DefaultJobDispatcher( app )
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/jobs/handler.py",
line 723, in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins(
self.app.config.server_name )
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/jobs/__init__.py",
line 671, in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ],
**runner.get( 'kwds', {} ) )
File
"/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/lib/galaxy/jobs/runners/pbs.py",
line 94, in __init__
assert pbs is not None, PBS_IMPORT_MESSAGE
AssertionError: The Python pbs-python package is required to use this
feature, please install it or correct the following error:
ImportError
/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/GALAXY/galaxy_dist/.venv/local/lib/python2.7/site-packages/pbs/_pbs.so:
undefined symbol: job_log_mutex
Removing PID file /var/run/galaxy/galaxy-job0.pid
Any ideas on how to solve this?
Thanks,
Tiago Macedo
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