Snakemake

Snakemake is my default workflow manager right now. Think of it like make - but designed for for the kind or work we actually do.

It's a Python library, so install via pip:

pip install snakemake

Verify Install

snakemake --version

which gives:

5.8.1

Warning

Notice that the Snakemake developers release new versions very frequently - and there can be breaking changes. Thus sometimes we may want a specific version installed. In this case, for example:

pip install snakemake==5.4.3

installs version 5.4.3 and uninstalls any existing version in the current environment.