A complete overhaul of the MAGOT toolkit. It will be a while before all functionality is ported over, but in the end it will be so much simpler and more elegantly written (and pip-installable).
pip install git+https://github.com/biorover/MAGOT2.git
#For list of subcommands, call:
MAGOT -h
#for subcommand help, call:
MAGOT <subcommand> -h