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/

Reply via email to