I'm trying to submit jobs to a supercomputer from a Rails application. Using ruby net/scp and net/ssh I've managed to upload contained simulations to the cluster. To start these jobs I would like to do:

ssh.exec! "csh /Volumes/RAID/Exoplanet/running_sims/system_id_5_sim_number_1/start_mercury.csh"

For some reason the ssh module I'm using won't operate outside the context of the users home directory.

If it did I could cd into the simulation root dir and do ./start_mercury.csh

In short is there a way to tell the script to operate within the context of its own directory and not use the users directory as its root?

It is difficult to give a more detailed reply without more details about the specific instance but, in general, you should be able to include some commands in the start script to source the desired user's profile and to change directory to that user's home (or wherever), if the permissions and groups for that user and the ssh user all match up ok.