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.
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