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That page is a bit out of date, the documentation is here: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