Re: [galaxy-dev] exporting environment variables to SGE in galaxy

On Jul 29, 2011, at 11:28 PM, Chaolin Zhang wrote:

Hi,

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

under sge_template = """#!/bin/sh #$ -S /bin/sh

but this did not help.

Any idea is very appreciated!

Chaolin

Chaolin, 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. -- Shantanu.