docker-compose.yml

version: '3.8'

services:
    redcap2sqlite:
        image: ghcr.io/im2neuroing/redcap2sqlite:main
        volumes:
        # folders to mount
        - ./newNeuroDMS/:/app/NeuroDMS/
        # files to mount needed for the configuration
        - ./REDCap2SQLite_config.json:/app/config.json:ro

        # (optional) mount the raw data csv file (if extraction is skipped - see example)
        - ./CLINICALDATA/Data/DBS_DATA.csv:/app/setup/DATA.csv
        # mount the entire mappingtables directory
        - ./CLINICALDATA/mappingTables:/app/setup/mappingtables:ro
        # mount the sqlite schema file
        - ./SQLite/sqlite_schema.sql:/app/setup/sqlite_schema.sql:ro
        # OPTIONAL: if you want to mount the output folder
        - ./newNeuroDMS/setup/:/app/data_setup/  #    "data_path": "data_setup/", to see the steps of the pipeline
        environment:
        - PYTHONUNBUFFERED=1

    image2sqlite:
        image: ghcr.io/im2neuroing/image2bids2sqlite:main-BIDS2SQLite
        volumes:
        # folder to mount
        - ./newNeuroDMS/:/app/NeuroDMS/ #Image management System folder which contains the BIDS folder
        # file to mount needed for the configuration
        - ./Image2BIDS2SQLite_config.json:/app/config.json:ro
        # file to mount needed for the schema (optional)
        - ./SQLite/sqlite_schema.sql:/app/sqlite_schema.sql:ro

        # OPTIONAL: if you want to mount the output folder
        - ./newNeuroDMS/setup/:/app/setup/  #    "extraction_path" : "/setup" to see the steps of the pipeline
        environment:
        # set the environment variables
        - PYTHONUNBUFFERED=1