Re: [galaxy-dev] change queue with sge
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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] change queue with sge
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 -- Sylvain Thomas tel : +33 (0)5 61 28 54 27 INRA - Unité de BIA Génopôle - plateforme Bio-informatique Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] change queue with sge
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] change queue with sge
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 -- Sylvain Thomas tel : +33 (0)5 61 28 54 27 INRA - Unité de BIA Génopôle - plateforme Bio-informatique Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
