To run this tutorial you will need anaconda or miniconda installed.
module load anaconda # Example to use on HPC
Create a conda environment using the environment.yml file:
conda env create --name snakemake --file environment.yaml
source activate snakemake
Once within the snakemake environment, execute the snakemake_setup.py script.
. snakemake_setup.py
This will run the download of cookiecutter as well as pull the slurm profile from https://github.com/Snakemake-Profiles/slurm. You will be prompted to provide default values-- you may leave these blank (recommended) or supply values.
This only needs to be run once per download of the workflow.
Execute a dry run in snakemake and check the total number of jobs required to run.
snakemake -np
Once dry run is successful and the configuration of your snakemake workflow is set up, run snakemake workflow.
snakemake --use-conda