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)

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

This ARMOR pipeline was used in Shayler et al. (2025) which can be accessed at: https://elifesciences.org/reviewed-preprints/101918v2#c65