Hi Peter,

Thanks for your answer.

No the galaxy machine is not a submitting node of the cluster. So I suppose I 
do have those two options:

(1) making the galaxy server a submitting node to the cluster
or
(2) install and run galaxy on a cluster node

What would be best? Any suggestions? If (1), any ideas on what needs to be 
installed?

Thanks.
Anne.

On 2 May 2012, at 21:26, Peter Cock wrote:

> On Wed, May 2, 2012 at 7:18 PM, Anne Pajon <anne.pa...@cancer.org.uk> wrote:
>> Hi,
>> 
>> I am struggling at integrating galaxy with our cluster. I am currently
>> running galaxy on a separate server machine from our LSF cluster.
>> The DRMAA library has been installed on the cluster and I've
>> re-installed galaxy into a shared file system visible and accessible
>> from both the server and the cluster.
> 
> That's good - the shared file system is highly recommended.
> 
>> ...
>> 
>> Am I right to think that there is no way to make the system
>> works because I cannot currently configure galaxy to ssh into
>> the cluster head node for submitting jobs to the scheduler?
>> 
>> ...
> 
> Is the Galaxy machine considered a submit node of the cluster?
> i.e. Can you submit/query/kill cluster jobs at the command line
> from the Galaxy server?
> 
> Peter

--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cancer.org.uk | +44 (0)7958 511 353


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