Installing Galaxy On Sge Cluster

Question: Installing Galaxy On Sge Cluster - Questions

6.2 years ago by

mailing list • 840 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? 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? Thanks, Greg

galaxy • 1.1k views

ADD COMMENT • link •

modified 6.2 years ago by Nate Coraor ♦ 3.2k • written 6.2 years ago by mailing list • 840

6.2 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

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). 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

ADD COMMENT • link written 6.2 years ago by Nate Coraor ♦ 3.2k

This makes sense, but I ultimately want to run the jobs as the logged in user as per this page: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_ Jobs_as_the_Real_User It wouldn't be feasible to add the virtualenv to every users' path. I'm hoping there's some kind of other way? Thanks again, Greg

ADD REPLY • link written 6.2 years ago by mailing list • 840

Indeed there is. Have a look at the 'environment_setup_file' option in the config file. --nate

ADD REPLY • link written 6.2 years ago by Nate Coraor ♦ 3.2k

@Nate, regarding "How will Galaxy know to use the virtualenv", I understand your suggestion "by setting the $PATH in the Galaxy user's ~/.bash_profile to include the virtualenv's bin directory (at the beginning of $PATH)". I noticed that some people use a different approach by adding "source ~/galaxy_env/bin/activate" to ~/.bash_profile. I was wondering if you could please explain the difference. Is one approach more reliable than the other? I'm in the process of installing Galaxy production on Ubuntu 14.04. Thanks!

ADD REPLY • link written 4.4 years ago by fire_water • 10

Similar posts • Search »