Unfortunately, there's a mistake in the sample config for that runner plugin,
the line to load the plugin should be:
<plugin id="drmaa" type="runner"
The sample config was fixed in a later commit to the stable branch, and seeing
as there was a security release today I would suggest just updating your Galaxy
installation to the latest stable commit anyway:
% hg pull
% hg update stable
On Apr 8, 2013, at 4:14 PM, Jingzhi Zhu wrote:
> I have downloaded the 04_01 release and tried to configure the Sun Grid
> Engine so that the job can run on our cluster.
> I have export the DRMAA_LIBRARY_PATH environment variable (export
> DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy
> job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on
> the plugins section so it looks like this in job_conf.xml
> <plugins workers="4">
> <!-- "workers" is the number of threads for the runner's work queue.
> The default from <plugins> is used if not defined for a <plugin>.
> <plugin id="local" type="runner"
> <plugin id="drmaa" type="runner"
> The run.sh returns the following error
> galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export
> tool: __EXPORT_HISTORY__
> galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import
> tool: __IMPORT_HISTORY__
> galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index
> tool: __GENOME_INDEX__
> galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler
> galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner
> galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner
> 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
> Traceback (most recent call last):
> line 37, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/app.py",
> line 159, in __init__
> self.job_manager = manager.JobManager( self )
> line 31, in __init__
> self.job_handler = handler.JobHandler( app )
> line 29, in __init__
> self.dispatcher = DefaultJobDispatcher( app )
> line 543, in __init__
> self.job_runners = self.app.job_config.get_job_runner_plugins()
> line 476, in get_job_runner_plugins
> runner_class = getattr( module, class_name )
> AttributeError: 'module' object has no attribute 'DRMAARunner'
> Can someone point to me what is going on here? If you have configured the SGE
> successfully with the latest 4.1 release, can you show me what the file
> job_conf.xml should look like? There are a lot of tags in this new XML file
> and I found it is hard to do it right.
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and other Galaxy lists, please use the interface at:
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