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.
looper templates, we must create a computing environment configuration file called
PEPENV. In short, you will need to:
PEPENVto the location of this file.
looper run --compute PACKAGE(where
PACKAGEis specified in your
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.