Hi,

is there anyone here who has any experience running galaxy with the queuing system SLURM? I've tried to install SLURM and a DRMAA module (http://apps.man.poznan.pl/trac/slurm-drmaa). I use the line:


$ export DRMAA_LIBRARY_PATH=/path/to/drmaa.so; python scripts/scramble.py DRMAA_python

The script compiles the egg nicely. When I try to start galaxy, it seems to be looking for SGE_ROOT though. Any thoughts?


Best regards,
Oscar Eriksson


Log file:
galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,127 Loaded external metadata tool: __SET_METADATA__ galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,132 Loaded indexer: INDEXER_Coverage_0 galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,137 Loaded indexer: INDEXER_Coverage_0 galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,142 Loaded indexer: INDEXER_Interval_0
galaxy.jobs.runners.local INFO 2011-02-09 15:42:27,143 starting workers
galaxy.jobs.runners.local DEBUG 2011-02-09 15:42:27,144 5 workers ready
Traceback (most recent call last):
File "/usr/ebiokit/galaxy/lib/galaxy/web/buildapp.py", line 82, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/usr/ebiokit/galaxy/lib/galaxy/app.py", line 72, in __init__
    self.job_manager = jobs.JobManager( self )
File "/usr/ebiokit/galaxy/lib/galaxy/jobs/__init__.py", line 41, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
File "/usr/ebiokit/galaxy/lib/galaxy/jobs/__init__.py", line 749, in __init__
    self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app )
File "/usr/ebiokit/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__
    self.ds.initialize()
File "/usr/ebiokit/galaxy/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 274, in initialize
    _w.init(contactString)
File "/usr/ebiokit/galaxy/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", line 59, in init
    return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File "/usr/ebiokit/galaxy/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check
    raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
InternalException: code 1: Please set the environment variable SGE_ROOT.

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