docker-compose.yaml

version: '3.8'
services:
  bifrost_db:
    image: mongo:4.4.2
    container_name: 'bifrost_db'
    restart: unless-stopped
    volumes:
      - ./bifrost_db:/data/db
    ports:
      - '27017:27017'
    environment:
      - MONGODB_DATA_DIR=/bifrost/bifrost_db
      - MONGO_INITDB_DATABASE=/bifrost_test_db # NOTE: testing requires the word 'test' to be in the DB name
      - MONGODB_LOG_DIR=/dev/null
    networks:
      - backend
  bifrostlib:
    build:
      context: '.'
      dockerfile: './lib/bifrostlib/Dockerfile'
      args:
        BUILD_ENV: dev
    volumes:
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/lib/bifrostlib
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py" --directory="/bifrost/lib/bifrostlib" -- pytest
  bifrost_run_launcher:
    build: 
      context: '.'
      dockerfile: './components/bifrost_run_launcher/Dockerfile'
      args: 
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_run_launcher
    volumes:
      - ./components/bifrost_run_launcher:/bifrost/components/bifrost_run_launcher
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_run_launcher
    entrypoint:
      # bash
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_run_launcher" -- pytest
  bifrost_min_read_check:
    build: 
      context: '.'
      dockerfile: './components/bifrost_min_read_check/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_min_read_check
    volumes:
      - ./components/bifrost_min_read_check:/bifrost/components/bifrost_min_read_check
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_min_read_check
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_min_read_check" -- pytest
  bifrost_cge_resfinder:
    build: 
      context: '.'
      dockerfile: './components/bifrost_cge_resfinder/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_cge_resfinder
    volumes:
      - ./components/bifrost_cge_resfinder/bifrost_cge_resfinder:/bifrost/components/bifrost_cge_resfinder/bifrost_cge_resfinder
      - ./components/bifrost_cge_resfinder/tests:/bifrost/components/bifrost_cge_resfinder/tests
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_cge_resfinder
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_cge_resfinder" -- pytest
  bifrost_cge_virulencefinder:
    build: 
      context: '.'
      dockerfile: './components/bifrost_cge_virulencefinder/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_cge_virulencefinder
    volumes:
      - ./components/bifrost_cge_virulencefinder/bifrost_cge_virulencefinder:/bifrost/components/bifrost_cge_virulencefinder/bifrost_cge_virulencefinder
      - ./components/bifrost_cge_virulencefinder/tests:/bifrost/components/bifrost_cge_virulencefinder/tests
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_cge_virulencefinder
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_cge_virulencefinder" -- pytest
  bifrost_chewbbaca:
    build: 
      context: '.'
      dockerfile: './components/bifrost_chewbbaca/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_chewbbaca
    volumes:
      - ./components/bifrost_chewbbaca/bifrost_chewbbaca:/bifrost/components/bifrost_chewbbaca/bifrost_chewbbaca
      - ./components/bifrost_chewbbaca/tests:/bifrost/components/bifrost_chewbbaca/tests
      - ./components/bifrost_assemblatron:/bifrost/components/bifrost_assemblatron
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_chewbbaca
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_chewbbaca" -- pytest
  bifrost_amrfinderplus:
    build: 
      context: '.'
      dockerfile: './components/bifrost_amrfinderplus/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_amrfinderplus
    volumes:
      - ./components/bifrost_amrfinderplus/bifrost_chewbbaca:/bifrost/components/bifrost_amrfinderplus/bifrost_amrfinderplus
      - ./components/bifrost_amrfinderplus/tests:/bifrost/components/bifrost_amrfinderplus/tests
      - ./components/bifrost_assemblatron:/bifrost/components/bifrost_assemblatron
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_amrfinderplus
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_amrfinderplus" -- pytest
  bifrost_whats_my_species:
    build: 
      context: '.'
      dockerfile: './components/bifrost_whats_my_species/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_whats_my_species
        FORCE_DOWNLOAD: 'false'
    volumes:
      - ./components/bifrost_whats_my_species:/bifrost/components/bifrost_whats_my_species
      # Note the resources file is ignored by .dockerignore due to it's size which is why it's mounted again.
      # - ./components/bifrost_whats_my_species/resources/:/bifrost/components/bifrost_whats_my_species/resources
      # NOTE: Docker ignore not working with context currently https://github.com/docker/compose/issues/1607, current hack used instead
      - $HOME/playground/bifrost/resources/bifrost_whats_my_species:/bifrost/components/bifrost_whats_my_species/resources
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_whats_my_species
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_whats_my_species" -- pytest
  bifrost_assemblatron:
    build: 
      context: '.'
      dockerfile: './components/bifrost_assemblatron/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_assemblatron
        FORCE_DOWNLOAD: 'false'
    volumes:
      - ./components/bifrost_assemblatron:/bifrost/components/bifrost_assemblatron
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_assemblatron
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_assemblatron" -- pytest
  bifrost_ssi_stamper:
    build: 
      context: '.'
      dockerfile: './components/bifrost_ssi_stamper/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_ssi_stamper
        FORCE_DOWNLOAD: 'false'
    volumes:
      - ./components/bifrost_ssi_stamper:/bifrost/components/bifrost_ssi_stamper
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_ssi_stamper
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_ssi_stamper" -- pytest
  bifrost_seqsero:
    build: 
      context: '.'
      dockerfile: './components/bifrost_seqsero/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_seqsero
    volumes:
      - ./components/bifrost_seqsero:/bifrost/components/bifrost_seqsero
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_seqsero
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_seqsero" -- pytest
  bifrost_enterobase:
    build: 
      context: '.'
      dockerfile: './components/bifrost_enterobase/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_enterobase
    volumes:
      - ./components/bifrost_enterobase:/bifrost/components/bifrost_enterobase
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
      - ENTEROBASE_USERNAME
      - ENTEROBASE_PASSWORD
      - ENTEROBASE_SERVER
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_enterobase
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_enterobase" -- pytest
  bifrost_salmonella_subspecies_dtartrate:
    build: 
      context: '.'
      dockerfile: './components/bifrost_salmonella_subspecies_dtartrate/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_salmonella_subspecies_dtartrate
    volumes:
      - ./components/bifrost_salmonella_subspecies_dtartrate:/bifrost/components/bifrost_salmonella_subspecies_dtartrate
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_salmonella_subspecies_dtartrate
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_salmonella_subspecies_dtartrate" -- pytest
  bifrost_cge_mlst:
    build: 
      context: '.'
      dockerfile: './components/bifrost_cge_mlst/Dockerfile'
      args:
        BUILD_ENV: dev
        BIFROST_COMPONENT_NAME: bifrost_cge_mlst
        FORCE_DOWNLOAD: 'false'
    volumes:
      - ./components/bifrost_cge_mlst/bifrost_cge_mlst:/bifrost/components/bifrost_cge_mlst/bifrost_cge_mlst
      - ./components/bifrost_cge_mlst/tests:/bifrost/components/bifrost_cge_mlst/tests
      - ./lib/bifrostlib:/bifrost/lib/bifrostlib
      - ./test_data/:/bifrost/test_data
      - ./bifrost_db:/bifrost/bifrost_db
    environment:
      - BIFROST_DB_KEY=mongodb://bifrost_db:27017/bifrost_test_db
    networks:
      - backend
    depends_on:
      - bifrost_db
    working_dir: 
      /bifrost/components/bifrost_cge_mlst
    entrypoint:
      watchmedo auto-restart --recursive --pattern="*.py;*.smk" --directory="/bifrost/components/bifrost_cge_mlst" -- pytest

networks:
  backend:
    driver: bridge
volumes:
  bifrost_db:
    driver: local