Hi Shantanu, Thanks for the information! This did the trick. Chaolin On Jul 30, 2011, at 1:28 AM, Shantanu Pavgi wrote:
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.