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Question: Installing Galaxy On A Cluster - What To Do About Python
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6.1 years ago by
mailing list • 840
mailing list • 840 wrote:
So I'm installing galaxy on our SGE cluster. I'm trying for the "unified" install option. We do have Python 2.6 installed on the cluster, but I'm not allowed to install any new libraries to it. Could anyone provide me with some basic directions on how to set it up with virtualenv? I've never used it before. And I'm using contrib/galaxy.fedora-init in init.d to start and stop the service. Would I need to reference virtualenv in there? Thanks, Greg
galaxy • 1.7k views
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modified 6.1 years ago by Carlos Borroto • 390 • written 6.1 years ago by mailing list • 840
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6.1 years ago by
Carlos Borroto • 390
Washington Metropolitan Area
Carlos Borroto • 390 wrote:
I do this by adding this to the ~/.bashrc file of the user running galaxy( in galaxy.fedora-init: RUN_AS="galaxy") source $HOME/env/bin/activate Hope it helps, Carlos
ADD COMMENT • link written 6.1 years ago by Carlos Borroto • 390
Thanks, but I'm confused. How will the cluster jobs galaxy submits know to use the virtual env? Or since all jobs are submitted as the galaxy user it will have the correct one? -Greg
ADD REPLY • link written 6.1 years ago by mailing list • 840
Greg, You can configure the environment for batch jobs in the file specified in the "environment_setup_file =" configuration directive. Regards, Alex
ADD REPLY • link written 6.1 years ago by Oleksandr Moskalenko • 30
You can do this or at least for SGE you can also use '-V' while configuring your job runner URL. drmaa://-V -q all.q/ Hope it helps, Carlos
ADD REPLY • link written 6.1 years ago by Carlos Borroto • 390
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