to run a snakemake pipeline:

1. enter project directory
2. cd to ARMOR directory
3. git pull origin master to be sure you have most update snakemake pipeline
4. conda activate ARMOR
5. snakemake -n --use-conda for a 'dry run'
6. snakemake -j 6 --use-conda for full run

• try running all of this inside a tmux sesssion
• if you get an error saying 'target cannot be locked', check to make sure that snakemake is not running elsewhere at the same time (probably in another tmux session)

to view all of the rules for a snakemake pipeline:

snakemake --rulegraph | dot -Tpdf > rulegraph.pdf