On Feb 1, 2012, at 9:13 PM, Derrick LIN wrote:
> Hi guys,
> Is there anyone has actually setup galaxy on a Rocks based cluster?
> I know that galaxy should be hosted on a submission host so that it can
> submit jobs to the cluster.
> Rocks provides preconfigured DRM such as SGE, so I start thinking if galaxy
> host should be deployed and managed by Rocks (e.g. as a Login Appliance in
> Rocks' term).
> Sorry if this is not a pure galaxy issue, but I guess people in here will be
> more appropriate to answer this.
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We have a similar setup. We had thought about creating galaxy appliance using
Rocks but we haven't done so yet. Instead our main galaxy instance is running
as a VM which is distinct from Rocks-SGE cluster. The galaxy VM is registered
as an SGE submit host with the SGE master host which is part of the Rocks
cluster. The cluster and the galaxy VM have a shared storage so our install
uses unified method as described on the galaxy wiki. The galaxy environment
(PATH, LD_LIBRARY_PATH, PYTHONPATH, TEMP_DIR etc..) is managed using
environment module files which we auto-load for 'galaxy' user using .bashrc
In addition to the main galaxy VM instance our cluster users can setup their
personal galaxy instances in their home directory for tool development or any
other work that's not currently supported in the main instance. And
users/developers can run galaxy tool wrappers directly from command-line if
I guess I have added too many details that you hadn't actually asked about.
But just wanted to share an overview of our galaxy install. Hope this is
Please keep all replies on the list by using "reply all"
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