Pronghorn - Snakemake SLURM Setup

This is setup for the SLURM scheduler for Snakemake Pipelines in Pronghorn.

Note: Please, use the latest Snakemake version (8.X)

• Step 1: Check the Snakemake version in your local pronghorn account by snakemake --version

• Step 2: If the version is 8.X, then please download the simple_v8/config.yaml file in it and upload it into the correct folder as follows. Create the directory structure using mkdir -p ~/.config/snakemake/simple_v8/ then cd ~/.config/snakemake/simple_v8/ Afterwards use wget or curl to download the config.yaml file:

wget https://raw.githubusercontent.com/Nevada-Bioinformatics-Center/pronghorn_snakemake_config/refs/heads/main/simple_v8/config.yaml

You may change the simple_v8 directory name to a name of your choice. Later, this will be your snakemake profile when executed.

• Step 3: Install the following commands

pip install snakemake-executor-plugin-slurm

and

pip install snakemake-executor-plugin-cluster-generic

• Step 4: Go to the folder/directory containing the Snakefile you wish to run.

• Step 5: Run the following command

  snakemake --profile simple_v8 --jobs 2 -n
  

  Here, --profile is the simple_v8 directory/folder name which house the config.yaml file, followed by the number of jobs --jobs which is 2. And -n is just for dryrun.