Installing Galaxy on a Cluster - What to do about Python
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
On Tue, Nov 6, 2012 at 2:27 PM, greg <margeemail@gmail.com> wrote:
Could anyone provide me with some basic directions on how to set it up with virtualenv? I've never used it before.
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
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 On Tue, Nov 6, 2012 at 3:12 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
On Tue, Nov 6, 2012 at 2:27 PM, greg <margeemail@gmail.com> wrote:
Could anyone provide me with some basic directions on how to set it up with virtualenv? I've never used it before.
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
On Nov 7, 2012, at 9:47 AM, greg <margeemail@gmail.com> wrote:
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
Greg, You can configure the environment for batch jobs in the file specified in the "environment_setup_file =" configuration directive. Regards, Alex
On Wed, Nov 7, 2012 at 9:52 AM, Oleksandr Moskalenko <om@hpc.ufl.edu> wrote:
On Nov 7, 2012, at 9:47 AM, greg <margeemail@gmail.com> wrote:
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
Greg,
You can configure the environment for batch jobs in the file specified in the "environment_setup_file =" configuration directive.
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
participants (3)
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Carlos Borroto -
greg -
Oleksandr Moskalenko