On Oct 2, 2012, at 12:45 PM, greg wrote:

> Hi guys,
> 
> I'm following the instructions here to install Galaxy on our SGE cluster.
> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
> (I'm aiming for the unified install)
> 
> Here are a couple of questions I'm hoping someone could clear up for me:
> 
> How exactly do I use virtual env to make Galaxy install all the Python
> libraries there instead of on the system?  How will Galaxy know to use
> the virtualenv to run and to use it for grid jobs?

Hi Greg,

You should start at the top level documentation for production servers:

    http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server

This includes instructions on how to set up a virtualenv.  You can make this 
the default by setting the $PATH in the Galaxy user's ~/.bash_profile to 
include the virtualenv's bin directory (at the beginning of $PATH).

> Do I need to install all of the dependencies listed on this page:
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
> If so what's a good way to make sure they're contained in the
> galaxy-dist directory and make sure Galaxy and all of the jobs know to
> find these tools there?

You only need to install the dependencies for the tools that you plan to use.  
Setting them up is explained in more detail here:

    http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies

--nate

> 
> Thanks,
> 
> Greg
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___________________________________________________________
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