Thanks for the information! This did the trick.
On Jul 30, 2011, at 1:28 AM, Shantanu Pavgi wrote:
On Jul 29, 2011, at 11:28 PM, Chaolin Zhang wrote:
> I am setting up SGE in our galaxy mirror. One problem I have is that I cannot export
environment variables of the specific users running the galaxy service. On command line,
I did this by qsub -V script.sh. or add a line
> #$ -V
> in script.sh
> I tried to change
> /lib/galaxy/jobs/runners/sge.py and lib/galaxy/jobs/runners/drmaae.py
> by adding a line
> #$ -V
> sge_template = """#!/bin/sh
> #$ -S /bin/sh
> but this did not help.
> Any idea is very appreciated!
I don't think you will need to modify source code for this. Adding "-V"
option to the drmaa URL should be sufficient. For example:
drmaa:// -V /
Hope this helps.