galaxy webserver jobs on a cluster

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galaxy webserver jobs on a cluster

Laure QUINTRIC
Hello,

We are facing some difficulties making the link between galaxy webserver
and our cluster.

As galaxy jobs are launched interactively with the user connected on
galaxy webserver on this webserver, how is it possible to use PBS qsub
command installed on the cluster to perform the job ?

Does PBS qsub has to be installed on the webserver also ?

In Galaxy documentation, there're the lines below :
"The underlying method for execution is “pluggable”. Currently jobs can
be executed on the same machine where the GALAXY instance is running, or
dispatched to a computational cluster using a standard queue manager
(portable batch system [PBS] is used at http://main.g2.bx.psu.edu),
however other dispatch strategies can be implemented and plugged in easily"

Can you give more information about these other dispatch strategies ?

Thanks for your help.

Laure

--
Laure QUINTRIC
Ifremer - IDM/RIC
Technopôle Brest-Iroise
29280 Plouzané
Tel: 02 98 22 49 11 - Fax : 02 98 22 46 47
E-mail : [hidden email]

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Re: galaxy webserver jobs on a cluster

Nate Coraor (nate@bx.psu.edu)
Laure QUINTRIC wrote:
> Hello,
>
> We are facing some difficulties making the link between galaxy
> webserver and our cluster.
>
> As galaxy jobs are launched interactively with the user connected on
> galaxy webserver on this webserver, how is it possible to use PBS
> qsub command installed on the cluster to perform the job ?

Hi Laure,

The Galaxy server will send jobs out as batch jobs when configured to do
so.

> Does PBS qsub has to be installed on the webserver also ?

The client software for whatever cluster scheduler you're using (Galaxy
is known to work with TORQUE PBS, SGE, and LSF, and should work with
other DRMAA-compliant schedulers) will need to be installed on the web
server, yes.

> In Galaxy documentation, there're the lines below :
> "The underlying method for execution is “pluggable”. Currently jobs
> can be executed on the same machine where the GALAXY instance is
> running, or dispatched to a computational cluster using a standard
> queue manager (portable batch system [PBS] is used at
> http://main.g2.bx.psu.edu), however other dispatch strategies can be
> implemented and plugged in easily"

That page is a bit out of date, the documentation is here:

  http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster

Prior to configuring a cluster instance, it's strongly recommended that
you implement the other Production Server steps:

  http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer

--nate

>
> Can you give more information about these other dispatch strategies ?
>
> Thanks for your help.
>
> Laure
>
> --
> Laure QUINTRIC
> Ifremer - IDM/RIC
> Technopôle Brest-Iroise
> 29280 Plouzané
> Tel: 02 98 22 49 11 - Fax : 02 98 22 46 47
> E-mail : [hidden email]
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>