On Tue, Apr 26, 2011 at 12:10 PM, Sean Davis <sdav...@mail.nih.gov> wrote:
> On Tue, Apr 26, 2011 at 5:11 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hi all,
>>
>> So far we've been running our local Galaxy instance on
>> a single machine, but I would like to be able to offload
>> (some) jobs onto our local SGE cluster. I've been reading
>> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
>>
>> Unfortunately in our setup the SGE cluster head node is
>> a different machine to the Galaxy server, and they do not
>> (currently) have a shared file system. Once on the cluster,
>> the head node and the compute nodes do have a shared
>> file system.
>>
>> Therefore we will need some way of copying input data
>> from the Galaxy server to the cluster, running the job,
>> and once the job is done, copying the results back to the
>> Galaxy server.
>>
>> The "Staged Method" on the wiki sounds relevant, but
>> appears to be for TORQUE only (via pbs_python), not
>> any of the other back ends (via DRMAA).
>>
>> Have I overlooked anything on the "Cluster" wiki page?
>>
>> Has anyone attempted anything similar, and could you
>> offer any guidance or tips?
>
> Hi, Peter.
>
> You might consider setting up a separate queue for SGE jobs. Then,
> you could specify a prolog and epilog script that will copy files from
> the galaxy machine into the cluster (in the prolog) and back to galaxy
> (in the epilog).

I see - the prolog and epilog scripts are per SGE queue, so
in order to have Galaxy specific scripts, the simplest solution
is a Galaxy specific queue.

> This assumes that there is a way to map from one
> file system to the other, but for Galaxy, that is probably the case
> (galaxy files on the galaxy server are "under" the galaxy instance and
> galaxy files on the cluster will probably be run as a single user in
> that home directory).

We have a user account "galaxy" on the Galaxy Server, and it would
make sense to have a matching user account "galaxy" on the Cluster
which would submit the SGE jobs and own their data files.

> I have not done this myself, but the advantage
> to using prolog and epilog scripts is that galaxy jobs then do not
> need any special configuration--all the work is done transparently by
> SGE.
>
> Sean

Thanks for the pointers - I have some reading ahead of me...

Peter

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