Run PEPATAC on a cluster

PEPATAC by itself does not specify any cluster resources, so you could just roll your own and submit individual jobs to a cluster however you choose. But because PEPATAC is already looper-compatible, the easier way is to use looper's built-in template system, which looper uses to build flexible shell scripts for job submission. These templates can be used to run jobs in a container, to submit to a cluster resource manager, or both.

To use looper templates, we must create a computing environment configuration file called PEPENV. In short, you will need to:

  • Set up a compute configuration file that includes a containerized or cluster compute template (or both).
  • Point the environment variable PEPENV to the location of this file.
  • Run the pipeline with looper run --compute PACKAGE (where PACKAGE is specified in your PEPENV file).

This enables you to adjust your computing preferences on-the-fly when you run a project.

The complete description of setting up looper to use PEPENV is generic to any pipeline. If you want to use looper with containers or clusters, you should consult the complete docs in the looper documentation on configuring looper to use a cluster.