On Mon, Nov 5, 2012 at 6:09 PM, Joel Rosenberg <thisisj...@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.

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