This lesson does not cover the specifics of using a Python IDE. As the instructor, you should be familiar 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). The only significant change is the
rm -f *.dat should be changed to
If students get lost, there is a hidden
.Snakemake file in the lesson
snakemake-lesson.tar.gz) that students can use
as a reference or use for the final “cluster submission” section.