Question: Installing Galaxy With Sge
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gravatar for Mariette
8.2 years ago by
Mariette30
Mariette30 wrote:
Hi everyone, 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 as following: # Comma-separated list of job runners to start. local is always started. If # left commented, no jobs will be run on the cluster, even if a cluster URL is # explicitly defined in the [galaxy:tool_runners] section below. The runners # currently available are 'pbs' and 'sge'. start_job_runners = sge # The URL for the default runner to use when a tool doesn't explicity define a # runner below. For help on the cluster URL format, see the ClusteringGalaxy # 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 mem=8G 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): File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/web/buildapp.py", 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 __init__ self.job_manager = jobs.JobManager( self ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/__init__.py", line 40, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/__init__.py", line 777, in __init__ self.job_runners[runner_name] = runners.sge.SGEJobRunner( app ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/runners/sge.py", line 83, in __init__ self.ds.init( self.default_cell ) File "build/bdist.linux-x86_64/egg/DRMAA.py", line 186, in init errParse(eno, estr) 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="">> ignored I'm guessing someting weird is happening with the DRMAA eggs, so I edited the /usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/runners/sge.py to 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 ? 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 ? thanks, Jerome
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