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.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
