Originally posted on galaxy-user:
I installed galaxy on our system and it worked just fine until I tryed
to settled it
up to make it run on our cluster. So I edited the universe_wsgi.ini file
# Comma-separated list of job runners to start. local is always
# left commented, no jobs will be run on the cluster, even if a cluster
# explicitly defined in the [galaxy:tool_runners] section below. The
# currently available are 'pbs' and 'sge'.
start_job_runners = sge
# The URL for the default runner to use when a tool doesn't explicity
# runner below. For help on the cluster URL format, see the
# Wiki. Leave commented if not using a cluster job runner.
default_cluster_job_runner = sge://INRA_CLC/wflowq//-R y -l h_vmem=8G -l
I also did the egg thing like this :
SGE_ROOT=/SGE/n1ge62 python2.5 scripts/scramble.py DRMAA_python
This line looks like it worked out.
Then when starting the engine, I'm catching this error :
Traceback (most recent call last):
line 61, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/app.py", line 69, in
self.job_manager = jobs.JobManager( self )
line 40, in __init__
self.dispatcher = DefaultJobDispatcher( app )
line 777, in __init__
self.job_runners[runner_name] = runners.sge.SGEJobRunner( app )
line 83, in __init__
self.ds.init( self.default_cell )
File "build/bdist.linux-x86_64/egg/DRMAA.py", line 186, in init
File "build/bdist.linux-x86_64/egg/DRMAA.py", line 167, in errParse
else: raise _errindex[errno-_errMin](errstring)
InvalidArgumentError: The input value for an argument is invalid.
Exception DRMAA.NoActiveSessionError: NoActiveSessionError('',) in
<bound method Session.__del__ of <DRMAA.Session object at 0x104e2bd0>>
I'm guessing someting weird is happening with the DRMAA eggs, so I
figure out if the module is
well loaded and sounds like it is ! So I'm kind of lost ... do you have
any idea on what is
going on ?
Did you get any further with this issue? The egg is definitely loading,
but this error is very strange - essentially, the library is complaining
that there's no active session when we try to create a new session,
which is what we want.
One other weird think is that I had to unset some tools from the
tool_conf.xml when starting
with the sge parameters, what hadn't to be done whitout sge, does it
sounds normal to you ?
galaxy-user mailing list