Question: Problem with SGE_ROOT, SGE / drmaa with Galaxy (updated)
0
danielfortin86 • 110 wrote:
Hi,
I'm trying to get my local Galaxy to submit jobs to an SGE cluster. However, I'm having problems with the configuration. I'm trying to use DRMAA but am getting an error that my SGE_ROOT isn't set, but I have set it. I've included the relevant lines from my paster.log, job_conf.xml and my $DRMAA_LIBRARY_PATH, $SGE_ROOT. Any suggestions would be greatly appreciated!
echo $DRMAA_LIBRARY_PATH
/usr/local/lib
echo $SGE_ROOT
/cm/shared/apps/sge/2011.11p1
paster.log:
galaxy.jobs.runners.state_handler_factory DEBUG 2016-02-24 11:21:04,767 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 64, in paste_app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
File "/opt/galaxy/lib/galaxy/app.py", line 142, in __init__
self.job_manager = manager.JobManager( self )
File "/opt/galaxy/lib/galaxy/jobs/manager.py", line 23, in __init__
self.job_handler = handler.JobHandler( app )
File "/opt/galaxy/lib/galaxy/jobs/handler.py", line 32, in __init__
self.dispatcher = DefaultJobDispatcher( app )
File "/opt/galaxy/lib/galaxy/jobs/handler.py", line 722, in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name )
File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 668, in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
File "/opt/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 83, in __init__
self.ds.initialize()
File "/opt/galaxy/eggs/drmaa-0.7.6-py2.6.egg/drmaa/session.py", line 257, in initialize
py_drmaa_init(contactString)
File "/opt/galaxy/eggs/drmaa-0.7.6-py2.6.egg/drmaa/wrappers.py", line 73, in py_drmaa_init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File "/opt/galaxy/eggs/drmaa-0.7.6-py2.6.egg/drmaa/errors.py", line 151, in error_check
raise _ERRORS[code - 1](error_string)
InternalException: code 1: Please set the environment variable SGE_ROOT.
Removing PID file paster.pid
job_conf.xml:
<?xml version="1.0"?>
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
</plugins>
<handlers> <handler id="main"/> </handlers>
<destinations default="SGE">
<destination id="local" runner="local"/>
<destination id="SGE" runner="drmaa">
<param id="nativeSpecification">-q all.q</param>
</destination>
</destinations>