Tutorial

  1. Edit config.yaml to include the following:

threads:

4

download_genbank:

options: “no”

tree_type:

options: “fasttree”

protein_dna:

options: “protein”

report:

“report.html”

previous_files:

“previous.fasta”

  1. Create genus.txt to include only the following (do not omit the quotes):

“Staphylococcus argenteus”

  1. Assure all the files are available in the correct folder and include an empty file named “previous.fasta”

  2. run:

snakemake –cores 4 (if 4 cores, 8 threads, are available)

  1. Have a hot drink and wait for the results!