The simplest way to learn to use this repo is to use these commands, and then learn what they do:
git clone --recurse-submodules https://github.com/GLYCAM-Web/AAD2_Docker.git
cd AAD2_Docker/
bash bin/build.bash
bash bin/run_test.bash
Note that the scripts in the bin directory are written to be run from the top-level directory (that is, from the directory where you find this file).