On Fri, Aug 24, 2012 at 1:25 PM, mailing list margeemail@gmail.com aka Greg wrote:
Thanks Assaf.
Would anyone know about my question 1? If I install a local version of Galaxy and connect it to our cluster, where is each user's (uploaded?) data stored? How will the cluster jobs be able to access the data?
By default, all the data is under a single folder, belonging to the galaxy Linux user account. We use /mnt/galaxy/galaxy-dist for this. In order that the cluster jobs can access the data, they must also be able to see this mount.
Galaxy does have support for staging files between file systems, but the simpler approach of unified storage is recommended. See http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
If anyone has installed galaxy and hooked it up to Sun Grid engine, I'd love to hear from you.
We're using Galaxy and SGE. You could run Galaxy on the SGE head node, but in our setup the Galaxy machine is just an SGE submit node (so it can submit jobs and check on them, i.e. you can use qsub and qstat from our Galaxy server).
Peter
P.S. It is very confusing that your emails give your name as "mailing list" rather than Greg.