What are the steps needed to setup the pipeline?

  1. Install dependencies
  2. Install required packages for R and Python
  • A shell script is provided to make the installation of the packages easy.
  • Run bash install/ from GAMER-pipeline directory
  • Users with a python2 virtual environment please activate before running the script
  1. Setup MySQL database for Pannzer
  • Create a database named pannzer
  • Create a user names pannzer and grant all privileges on the database pannzer
  • The password should be pannzer
  • If you decide to change any of this, please update the config.json [mix-meth.PANNZER.database] file accordingly.