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 ___________________________________________________________ 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: