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Workflows using Snakemake

LOCATION: INSCC Auditorium (Room 110)
DATE: Tuesday, March 24, 2020

TIME: 1:00 p.m. - 3:00 p.m.

Presented by Brett Milash

To join via Zoom:

meeting ID 411 178 3659

To call  in:

+1 408 638 0968
+1 646 876 9923
+1 669 900 6833


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.


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


The slides are available here: workflows_with_snakemake.pdf

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 "") and execute the following commands:

module load git

git clone

Last Updated: 3/24/20