I'll take a couple of stabs at this. First, make sure that /scratch/galaxy 
exists.
There's an error at the bottom of your pastie that seems to indicate it's not 
there.
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.

-Scott

----- Original Message -----
> So here is what I've installed so far.  (/usr/local/galaxy) is a
> directory that all nodes in the cluster can see.  And the web server
> machine can also see it.)
> 
> $ls -l /usr/local/galaxy
> drwxrwxr-- 20 galaxy  scicomp 2206 Nov  8 15:53 galaxy-dist
> -rwxrwxr-x  1 galaxy  scicomp 1882 Nov  8 15:34 galaxy.fedora-init
> drwxr-xr-x  5 galaxy scicomp   67 Nov  8 10:08 galaxy_python
> -rw-r--r--  1 galaxy scicomp   80 Nov  8 15:32
> job_environment_setup_file
> drwxrwxr--  2 galaxy  scicomp   28 Nov  8 15:43 logs
> 
> Here are are the changes I made to galaxy-dist/universe_wsgi.ini
> http://pastie.org/5351347
> 
> Here is what I put in my job_environment_setup_file:
> export TEMP=/scratch/galaxy
> source /usr/local/galaxy/galaxy_python/bin/activate
> 
> The galaxy_python directory contains my virtual env based off of
> Python 2.7.
> 
> Finally here are the contents of my galaxy.fedora-init file:
> http://pastie.org/5351396
> 
> (Note: I created a sym link in /etc/init.d/ to
> /usr/local/galaxy/galaxy.fedora-init
> Then ran chkconfig --add galaxy.fedora-init
> So I can use sudo /sbin/service galaxy.fedora-init start/stop)
> 
> 
> Here are the results from running:
> $sudo /sbin/service galaxy.fedora-init start
> http://pastie.org/5351308
> 
> So my first question is why does it appear to be using Python 2.6?
>  Is
> it not using my virtual env?  Am I using virtual env incorrectly?
> 
> Thanks,
> 
> Greg
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