Run galaxy on a specific SGE queue

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Run galaxy on a specific SGE queue

sarah Maman
Hi everyone,
Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one.

To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following:
default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/

When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q.
Should be the queue setting this way ? What are we doing wrong ?

thanks for your help,
Sarah
Sarah Maman
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53

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Re: Run galaxy on a specific SGE queue

Nate Coraor (nate@bx.psu.edu)
On May 22, 2013, at 11:36 AM, Sarah Maman wrote:

> Hi everyone,
> Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one.
>
> To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following:
> default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/
>
> When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q.
> Should be the queue setting this way ? What are we doing wrong ?

Hi Sarah,

Without knowing what's going on in your environment I can't say for sure, but I would guess that something else is (~/.sge_request?) is also attempting to set the queue.  Are you able to use `qsub -q test.q` on the command line as the same user that runs Galaxy?

Thanks,
--nate

>
> thanks for your help,
> Sarah
> Sarah Maman
> INRA - LGC - SIGENAE
> Chemin de Borde-Rouge - Auzeville - BP 52627
> 31326 Castanet-Tolosan cedex - FRANCE
> Tel:   +33(0)5.61.28.57.08
> Fax:   +33(0)5.61.28.57.53
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


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Re: Run galaxy on a specific SGE queue

Sarah Maman-2
Thanks Nate,

In fact,  our ~/.sge_request  set workq by default.
So, we have changed this parameter in  ~/.sge_request file in order to change the working queue.

Thanks again for your help,
Sarah




Nate Coraor a écrit :
On May 22, 2013, at 11:36 AM, Sarah Maman wrote:

  
Hi everyone,
Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one.

To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following:
default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/

When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q.
Should be the queue setting this way ? What are we doing wrong ?
    

Hi Sarah,

Without knowing what's going on in your environment I can't say for sure, but I would guess that something else is (~/.sge_request?) is also attempting to set the queue.  Are you able to use `qsub -q test.q` on the command line as the same user that runs Galaxy?

Thanks,
--nate

  
thanks for your help,
Sarah
Sarah Maman
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08 
Fax:   +33(0)5.61.28.57.53
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
    

  


-- 
          --*--
Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53 
         --*--

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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