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!


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