Hi Jingzhi,
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" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
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
--nate
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" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> </plugins>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 workers 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): File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", 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 ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins() File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", 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.
Thanks!
Jingzhi
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