This lesson is in the early stages of development (Alpha version)

Getting Started with Snakemake: Instructor Notes

This lesson does not cover the specifics of using a Python IDE. As the instructor, you should be familar with the editor you intend to teach, as well as how to install/set it up across all three platforms (Windows, MacOS, Linux). If you don’t have a preference for one editor over another, we recommend using either Jupyter Notebooks, Spyder, or a text editor/IPython console (because these come preinstalled with Anaconda).

You have the option of running the Snakemake portion of the workshop either on student laptops or an HPC cluster. If you end up going the laptop route, be aware of how to run things via the Windows command line (since Snakemake natively works on Windows). Affected commands are:

Running in Git Bash on Windows is another option that should allow all Linux command-line operations to work as-is. See the setup page for details.

Solution Files

If students get lost, there are solutions to most episodes in the .solutions directory included in the downloadable files.

C3DIS 2020 Notes

For the C3DIS2020 workshop, the cluster submission episode will be skipped due to the workshop only being delivered on student laptops. The material is included for self-study after the workshop concludes.