On Mon, Nov 5, 2012 at 6:09 PM, Joel Rosenberg <thisisjoel@hotmail.com> wrote:
Thanks Peter,
I tried doing something similar, but there wasn't a location in the galaxy user's $PATH that would persist across a cluster reboot or could be snapshotted (like the tools or data volumes). Adding /mnt/galaxyTools/my_dep_binaries or something to the $PATH would work temporarily, but not past a reboot as /home/galaxy/.bashrc, /etc/environment, etc are part of the AMI and would be lost.
In your cluster, wouldn't the galaxy user's ${HOME}/bin be transient? Are you running with a different EC2 setup or using a different AMI?
We're running a local cluster with SGE, and that means our $HOME/bin is stable. I hadn't realised this you mentioned EC2/AMI that you might be on a cloud cluster. Peter