Please see https://github.com/phbradley/conga for the latest version of CoNGA and instructions.
This version incorporates the OLGA package find the generational probabilities that are used by CoNGA as a TCR feature. It works but due to these calculations is very slow on large datasets. If you stumble across this and you're interested in using Pgen as a feature, let us know!
OLGA needs to be installed within your CoNGA conda environment
conda activate conga_env
pip install olga