I recently wrote a shell script for a colleague which describes, using comments and commands, how to generate a random gene tree and DNA sequences for its leaves. I chose the shell script format to reduce the amount of stuff to explain, but it would be convenient for the user to have Snakemake rules for running the commands instead.
For this exercise, download
- a JAR file containing code for generating random trees, and
- a shell script with instructions for how to use the JAR file.
Try the shell script first to make sure it works for you. Then, try to rewrite the functionality with Snakemake!