What are the steps needed to setup the pipeline?¶
- Install dependencies
- Install required packages for R and Python
- A shell script is provided to make the installation of the packages easy.
bash install/install_packages.shfrom GAMER-pipeline directory
- Users with a python2 virtual environment please activate before running the script
- 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
- If you decide to change any of this, please update the config.json [mix-meth.PANNZER.database] file accordingly.