Andreas Kuntzagk wrote:
It is set in ~/.bashrc, which is source by ~/.bash_profile. If I normally login to a cluster node via ssh it is set correctly. But if I qsub a job, it is not read. Except when I set the "-V" switch. So I either need to change gridengines behaviour or make galaxy use that switch.
Is there a easy way to config how to submit cluster jobs?
SGE must not be running the shell as a login or interactive shell, which PBS does. You may want to check the 'INVOCATION' section of the bash(1) man page to see how you can force this.
If you can't change how your shell is run by SGE, you could add what you need to the SGE job template in:
but this would be an ugly hack.