snakemake_profiles

snakemake profiles to atapt snakemake to run in specific cluster configurations

• Version: 0.1.0
• Authors:
  • Nick Youngblut [email protected]
• Maintainers:
  • Nick Youngblut [email protected]

Description

For an intro into snakemake profiles, see the snakemake docs

This repo only contains a couple of custom profiles that have been tested to work with the clusters used by members of the Ley Lab. For more (generalized) profiles, see the snakemake-profiles repo

Profiles

SGE cluster

Copy the sge directory from this repo to ~/.config/snakemake/:

$ mkdir -p ~/.config/snakemake/
$ chmod u+x sge/*.py 
$ cp -r sge ~/.config/snakemake/

SLURM cluster

Copy the slurm directory from this repo to ~/.config/snakemake/:

$ mkdir -p ~/.config/snakemake/
$ chmod u+x slurm/*.py 
$ cp -r slurm ~/.config/snakemake/