Last updated: 2023-09-21
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Knit directory: snakemake_tutorial/
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This website contains a short introduction to Snakemake intended for a biostatistics/statistical genetics audience. This tutorial is intended to be a “quick start”. We should be able to cover this material in about an hour. With the material in this tutorial, you will be able to write a basic Snakemake pipeline and execute it either locally or on a cluster.
Due to time constraints, there is lots of material that we won’t cover in this guide. Once you are started, there are several excellent resources for learning more.
This website was created for a tutorial given at the University of Michigan, so some instructions specifically reference U of M computing resources.
Snakemake resources:
Other resources:
In this tutorial, I will assume that you are using a computer with either a Linux or Mac operating system. If your personal computer runs Windows, I recommend doing this tutorial on one of the clusters available to you (e.g. the Biostatistics department cluster, the CSG cluster, or Great Lakes). It is possible to run Snakemake on Windows, but I do not have very much experience with this.