Running R with Slurm

[jdlamstein]

Hi all,

I’m running galaxy on a compute cluster with Slurm and I’m having trouble running R. We have python running with the .venv, but the only way I’ve been able to run R is by install R on a node, which isn’t sustainable. What do you recommend for setting up R for galaxy with slurm?

Thanks!

[jennaj]

Hi @jdlamstein

I think the solution is to run a Conda .venv, and to not use a Python .venv. From the start, so that everything else in the local configuration also uses it.

But you can decide. The “Python” way will make not just R difficult to manage but also many other dependencies troublesome. Others can correct me (and share back how) if some hybrid works for them.

References:

• Galaxy Documentation — Galaxy Project 23.0.2.dev0 documentation
  • See here first → Framework Dependencies — Galaxy Project 23.0.2.dev0 documentation
• Galaxy Training — Admin
  • Then see here → Connecting Galaxy to a compute cluster

Hope that helps!