Question: galaxy crashes trying to load pbs-python, possibly related to visualization
gravatar for wrf
3.6 years ago by
wrf0 wrote:


Our Galaxy instance has not been able to restart since this morning. Looking at the logs, the only thing that has changed lately was when I had attempted to configure a new visualization. Then, restarting Galaxy with hit this error (including a few previous lines): DEBUG 2015-04-22 13:46:11,164 Loaded history import tool: __IMPORT_HISTORY__
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,165 VisualizationsRegistry, loaded plugin: charts
galaxy.visualization.registry INFO 2015-04-22 13:46:11,166 <galaxy.visualization.registry.VisualizationsConfigParser object at 0x7f8238d7ec50>, plugin disabled: Circster. Skipping...
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,167 VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,167 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,168 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.registry INFO 2015-04-22 13:46:11,169 <galaxy.visualization.registry.VisualizationsConfigParser object at 0x7f8238d7ec50>, plugin disabled: Sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,170 VisualizationsRegistry, loaded plugin: trackster DEBUG 2015-04-22 13:46:11,170 Starting job handler INFO 2015-04-22 13:46:11,170 Handler 'main' will load all configured runner plugins DEBUG 2015-04-22 13:46:11,171 Loaded 'failure' state handler from module DEBUG 2015-04-22 13:46:11,171 Starting 4 LocalRunner workers DEBUG 2015-04-22 13:46:11,171 Loaded job runner '' as 'local'
Traceback (most recent call last):
  File "/var/project/galaxy-dist/lib/galaxy/webapps/galaxy/", line 44, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/var/project/galaxy-dist/lib/galaxy/", line 136, in __init__
    self.job_manager = manager.JobManager( self )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/", line 23, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/", line 32, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/", line 715, in __init__
    self.job_runners = )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/", line 586, in get_job_runner_plugins
    module = __import__( module_name )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/runners/", line 32, in <module>
    raise Exception( egg_message % str( e ) )

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:

Additional errors may follow:

At the moment I cannot use the web server, so I cannot configure anything there. Is there some way to disable the visualization temporarily (like some flag to change to FALSE somewhere)? Does anyone know what might cause this problem, if it is not the visualization?

Many thanks!

error crash galaxy pbs • 1.6k views
ADD COMMENTlink modified 3.6 years ago by carlfeberhard390 • written 3.6 years ago by wrf0
gravatar for Nate Coraor
3.6 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Galaxy loads job plugins based on what's configured in the job configuration file, by default config/job_conf.xml, although this can be changed by setting job_config_file in galaxy.ini. I'd suggest checking to make sure that you did not inadvertently enable the PBSJobRunner.

ADD COMMENTlink written 3.6 years ago by Nate Coraor3.2k

That was indeed the problem. Thanks!

ADD REPLYlink written 3.6 years ago by wrf0
gravatar for carlfeberhard
3.6 years ago by
United States
carlfeberhard390 wrote:

Hi, wrf

Reading the Traceback it looks like the problem has more to do with your copy of pbs_python and not the visualization. The last lines of a traceback will generally give you the file and line number within that file where the error occurred. From there you can use it to trace back the steps that (possibly) caused the error.

The help provided in the error message mentions the wiki location for more information on how to build an configure your job runners and, more specifically for your case, pbs_python:

From what I can tell you or your admin may need to re-compile pbs_python.

If you are still concerned that it is the visualization registry: you can edit your config/galaxy.ini file, uncomment the 'visualization_plugins_directory' line, and set it to None:  visualization_plugins_directory = None. This will disable *all* visualizations from loading and being shown as options in the history.

ADD COMMENTlink written 3.6 years ago by carlfeberhard390

we are using SLURM on a gentoo system, so I'm not sure that PBS was ever configured in the first place as it is incompatible with SLURM. What would I disable to stop it from trying to load PBS?

ADD REPLYlink written 3.6 years ago by wrf0
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