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 > <[email protected]> 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 > ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
