Run on OSC

Running the workflow on the OSC SLURM Cluster.

The following commands should be run from a login node after cloning this repo and changing into that directory.

Install Snakemake

The following commands

• load the conda environment module
• create the snakemake conda environment
• unload the conda environment module

module load miniconda3/23.3.1-py310
conda create -c conda-forge -c bioconda -n snakemake snakemake=7.32.4 mamba=1.5.3 -y
module purge

Run Workflow

Before running you may want to change the config/config.yaml limit_images: 20 setting to limit_images: "" to process the entire dataset.

The following commands

• load the conda environment module
• activate the snakemake conda environment
• start the sbatch job

module load miniconda3/23.3.1-py310
source activate snakemake
sbatch --account=PAS2136 run-workflow.sh