Andreas Kuntzagk wrote:
As far as I understand your galaxy and gridengine need to share some NFS. The solution I use is to run galaxy on a computer which is a submit host of the cluster and thus has access to sge binaries and have the webserver reverse-proxy the galaxy site. So if you run galaxy on your head node you just need to pass HTTP traffic through your firewall. For using apache as a proxy see: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy For general "production server nodes: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer And for integrating SGE: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
Thanks Andreas. Matt, SGE must exist on the Galaxy server since you need access to $SGE_ROOT to submit and monitor jobs. It does not need to be the same machine as the head node, but the SGE commands need to work and to use some sort of NFS as explained by Andreas since this is how the cluster is able to access the same files as the Galaxy server. --nate