30 Jul
2011
30 Jul
'11
6:28 a.m.
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