Workflows using Snakemake

Description

Snakemake is a work flow tool, implemented in python, that helps you create parallel, modular work flows and run them on a SLURM cluster. In this 2-hour hands-on session we will create and run several simple work flows, examine their graphical output, and execute them on a SLURM cluster at CHPC.

Prerequisites

To get the most from this workshop you should have the following:

• a laptop that can connect to the campus WiFi
• a CHPC account
• some familiarity with the shell command line and shell scripting
• the ability to use a text editor
• a little familiarity with python
• familiarity with SLURM commands for submitting jobs to a cluster

Materials

The slides are available here: workflows_with_snakemake.pdf

The exercises and solutions are located here: https://github.com/CHPC-UofU/workflows-with-snakemake

To download the exercises and solutions, log in to your CHPC account on one of the frisco nodes (which are numbered 1-8, for example "frisco3.chpc.utah.edu") and execute the following commands:

module load git

git clone https://github.com/CHPC-UofU/workflows-with-snakemake.git