There are two slightly different problems here. One with the files ystem
and the second is whether the machine Galaxy is running on can submit
jobs to the cluster (ssh is mentioned in the original e-mail, suggesting
that it's impossible to communicate with the cluster from the machine
the job is running on). The Galaxy instance is constantly communicating
with the cluster job scheduling system (SGE or other) in order to get
updates on the status of the jobs. It should be possible to do it over
ssh, but, in my experience, this slows down the code.
We run the Galaxy server on one of the cluster nodes. I imagine that
other people using Galaxy with the cluster do the same. Are they?
Marina
On 15/06/2011 08:51, Peter Cock wrote:
On Wed, Jun 15, 2011 at 2:30 AM, Ka Ming Nip<km...@bcgsc.ca> wrote:
Hello,
I have been trying to set up Galaxy to run its jobs on my SGE
cluster using the Unified Method, based on the steps described
in the wiki:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
My local instance of Galaxy is installed under my home directory,
but my cluster is on a different file system. I need to "ssh" to the
head node before I can submit jobs.
Is there any way to set up Galaxy with a SGE cluster on a different
file system?
I haven't looked into it in great detail, but we currently have a
similar network setup, and would also like to link Galaxy to SGE.
The main problem is the lack of a shared file system - in order
to run a job on the cluster we (Galaxy) has to get the data onto
the cluster, run the job, and get the results back.
Peter
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