Hi
I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one.
Does anyone has solved this problem?
Thanks,
Sylvain
On 05/03/2011 03:11 PM, Sylvain Thomas wrote:
Hi
I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one.
Here is what i use :
start_job_runners = drmaa default_cluster_job_runner = drmaa://-q galaxy -V/
Regards,
Jean-Baptiste
When I use : default_cluster_job_runner = drmaa://-q longq -V/
I obtain this error :
/DeniedByDrmException: code 17: Multiple different queues - longq workq - found. Job rejected./
workq is our default queue. It seems that it doesn't overwrite the queue but if an user type : qsub -q longq.... there is no problem.
Regards,
Sylvain
Le 03/05/2011 15:34, Jean-Baptiste Denis a écrit :
On 05/03/2011 03:11 PM, Sylvain Thomas wrote:
Hi
I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one.
Here is what i use :
start_job_runners = drmaa default_cluster_job_runner = drmaa://-q galaxy -V/
Regards,
Jean-Baptiste
Hi
Hi
I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one.
I've just configured my Galaxy instance to work to submit to a specific LSF queue. I am passing native specification LSF options to be used with drmaa. The relevant part of my universe_wsgi.ini looks like this:
# The URL for the default runner to use when a tool doesn't explicitly define a # runner below. default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/
where -q srpipeline defines the queue and -P pipeline defined the project name.
SGE native specification options might be different, you'll have to look in the SGE docs
Setting the queue with an env variable does not work for me and leads to a segmentation fault due to a bug inside the lsf-drmaa library
Marina
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