So I ended up moving these lines:

export DRMAA_LIBRARY_PATH=/sge/current/lib/lx-amd64/libdrmaa.so
export TEMP=/scratch/galaxy
source /usr/local/galaxy/galaxy_python/bin/activate

from galaxy.fedora-init to the galaxy user's .bashrc file.
(/home/galaxy/.bashrc)

It seems to be working, I see the virtual env on the python path in
the log file so I think it's working.

Now I'm on to a database connection problem.  Thanks for the help!

-Greg

On Fri, Nov 9, 2012 at 3:09 PM, Scott McManus <scottmcma...@gatech.edu> wrote:
>
> Whoops. I missed that (obviously).
>
> When you use "su", you preserve the existing environment. When you use
> "su -", you use the root environment and discard the calling user's
> environment. So I'm guessing that what's happening in the "start" command
> is that the "su -" is dumping the previous env.
>
> You could try prepending the virtualenv to the command that is executed
> as part of "-c":
> cmd="source /usr/local/galaxy/galaxy_python/bin/activate; cd $RUN_IN && sh 
> run.sh --daemon --log-file /usr/local/galaxy/logs/galaxy.log"
> (I'm not proud of that, but it might work.)
>
> -Scott
>
> ----- Original Message -----
>> On Fri, Nov 9, 2012 at 2:40 PM, Scott McManus
>> <scottmcma...@gatech.edu> wrote:
>> >
>> > Second, you're right about virtualenv not being used. It is likely
>> > that root
>> > is being used, which means that all of the virtualenv stuff for the
>> > galaxy user
>> > won't be available. I haven't tried this, but you could try
>> > modifying your
>> > galaxy.fedora-init to contain a call to virtualenv - that way you
>> > switch into the
>> > proper sandbox when you startup.
>>
>> Thanks Scott.  I think I already have that call in there.  That's why
>> I'm so confused.  See line 21 http://pastie.org/5351396
>>
>> Is something not working with that call.  Maybe that call affects
>> root
>> and not the galaxy user?
>>
>> -Greg
>>
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