Snakemake is a popular workflow management tool that can help organize, document, scale, run, and reproduce your workflows. Snakemake workflows are described via a human-readable, Python-based language, and can be integrated into SCINet high-performance computing (HPC) clusters via Slurm and Conda.
In this workshop, Aaron Yerke (SCINet/AI-COE fellow) will introduce the basics of a Snakemake workflow and demonstrate how to run it on a SCINet cluster. After attending this workshop, you should be able to integrate Snakemake into your own projects on SCINet HPC clusters.
Pre-Workshop Instructions:
To help minimize technical issues and delays at the start of the workshop, please try the following tests prior to the workshop.
- Logging on to Ceres Open OnDemand (OOD):
- Please confirm you can successfully log in to Ceres OOD with your SCINet account (see login instructions here). If you are successful, you will be able to see the Ceres OOD home page.
- Ceres Shell Access:
- When on Ceres OOD, click on the top navigation bar: “Clusters” > “Ceres Shell Access”. A new tab will appear that looks like a shell terminal (e.g., like PowerShell).
- Please confirm you do not receive any error messages or requests to re-authenticate and that the final line looks like “[firstname.lastname@ceres ~]$”.
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Introduction to Snakemake
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Individual Snakemake assistance