So fare there is no final comandline option and installation. The Pipeline can be run from the combandline by editing the run_pipelin.py file for the first part and the run_pipeline_2.py file for the second part.
The entitynetwork folder contains the main part of the code. The subfolder names point to their purpose for the Pipeline. The main file, combining the different modules of the Pipeline it in the entity_netowrk_pipeline folder, the process_article.py file.