docker-compose.yml

 version: '2'

 services:
    biomaj-mongo:
        image: mongo:3.2
        volumes:
            - ${BIOMAJ_DIR}/mongo:/data/db

    biomaj-redis:
        image: redis
        volumes:
            - ${BIOMAJ_DIR}/redis:/data

    biomaj-elasticsearch:
        image: "elasticsearch:2"
        command: "elasticsearch -Des.cluster.name='biomaj'"

    biomaj-rabbitmq:
        image: rabbitmq
        hostname: biomaj-rabbitmq
        command: rabbitmq-server
        entrypoint: ""
        volumes:
            - ${BIOMAJ_DIR}/rabbitmq:/var/lib/rabbitmq
            - ${BIOMAJ_DIR}/biomaj-config/rabbitmq.config:/etc/rabbitmq/rabbitmq.config:ro
        environment:
            - RABBITMQ_DEFAULT_USER=biomaj
            - RABBITMQ_DEFAULT_PASS=biomaj

    biomaj-consul:
        image: hashicorp/consul:1.17
        hostname: consulnode1
        ports:
            - "8400:8400"
            - "8500:8500"
            - "8600:53"
        command: agent -dev -client 0.0.0.0 -log-level info

    biomaj-prometheus:
        image: prom/prometheus:v2.45.6
        ports:
            - "9090:9090"
        volumes:
            - ${BIOMAJ_DIR}/biomaj-config/prometheus.yml:/etc/prometheus/prometheus.yml
        depends_on:
            - biomaj-consul
        command:
            - '--storage.tsdb.retention.time=720h'
            - '--config.file=/etc/prometheus/prometheus.yml'

    biomaj-influxdb:
        image: influxdb
        volumes:
            - ${BIOMAJ_DIR}/influxdb:/var/lib/influxdb
        environment:
            - INFLUXDB_DB=biomaj
            - INFLUXDB_USER=biomaj
            - INFLUXDB_PASSWORD=biomaj

    biomaj-public-proxy:
        # In production, port 8080 should not be open
        image: traefik:1.7
        ports:
            # - "8080:8080"
            - "5000:80"
        volumes:
            - ${BIOMAJ_DIR}/proxy/traefik/traefik.toml:/etc/traefik/traefik.toml
            - /var/run/docker.sock:/var/run/docker.sock
        depends_on:
            - biomaj-consul

    biomaj-internal-proxy:
        # In production, ports should not be open
        image: traefik:1.7
        #ports:
        #        - "8082:8080"
        #        - "8081:80"
        volumes:
                - ${BIOMAJ_DIR}/proxy/traefik/traefik-int.toml:/etc/traefik/traefik.toml
        depends_on:
            - biomaj-consul

    biomaj-user-web:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajuser
            - WAIT_HOSTS=biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-redis
        command: ["/startup.sh", "gunicorn",  "-b",  "0.0.0.0:5000", "--log-config", "/etc/biomaj/production.ini biomaj_user.wsgi:app"]

    biomaj-download-web:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajdownload
            - WAIT_HOSTS=biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-redis
        command: ["/startup.sh", "gunicorn", "-c", "/etc/biomaj/gunicorn_conf.py", "-b", "0.0.0.0:5000", "--log-config", "/etc/biomaj/production.ini biomaj_download.biomaj_download_web:app"]

    biomaj-download-message:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajdownload
            - RABBITMQ_USER=biomaj
            - RABBITMQ_PASSWORD=biomaj
            - WAIT_HOSTS=biomaj-rabbitmq:5672, biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-rabbitmq
            - biomaj-redis
        command: ["/startup.sh", "biomaj_download_consumer.py"]

    biomaj-process-web:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
            - ${BIOMAJ_DIR}/biomaj/process:/opt/conda/envs
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajprocess
            - WAIT_HOSTS=biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-redis
        command: ["/startup.sh", "gunicorn", "-c", "/etc/biomaj/gunicorn_conf.py", "-b", "0.0.0.0:5000", "--log-config", "/etc/biomaj/production.ini biomaj_process.biomaj_process_web:app"]

    biomaj-process-message:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
            - ${BIOMAJ_DIR}/biomaj/process:/opt/conda/envs
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajprocess
            - RABBITMQ_USER=biomaj
            - RABBITMQ_PASSWORD=biomaj
            - DOCKER_URL=${DOCKER_URL}
            - WAIT_HOSTS=biomaj-rabbitmq:5672, biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-rabbitmq
            - biomaj-redis
            - biomaj-elasticsearch
        command: ["/startup.sh", "biomaj_process_consumer.py"]

    biomaj-daemon-web:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajdaemon
            - RABBITMQ_USER=biomaj
            - RABBITMQ_PASSWORD=biomaj
            - WAIT_HOSTS=biomaj-redis:6379, biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-rabbitmq
            - biomaj-redis
            - biomaj-influxdb
            - biomaj-elasticsearch
            - biomaj-user-web
            - biomaj-download-web
            - biomaj-process-web
        command: ["/startup.sh", "gunicorn", "-c", "/etc/biomaj/gunicorn_conf.py", "-b", "0.0.0.0:5000", "--log-config", "/etc/biomaj/production.ini biomaj_daemon.daemon.biomaj_daemon_web:app"]

    biomaj-daemon-message:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajdaemon
            - RABBITMQ_USER=biomaj
            - RABBITMQ_PASSWORD=biomaj
            - WAIT_HOSTS=biomaj-redis:6379, biomaj-mongo:27017, biomaj-consul:8500, biomaj-rabbitmq:5672
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-rabbitmq
            - biomaj-redis
            - biomaj-elasticsearch
            - biomaj-user-web
            - biomaj-download-web
            - biomaj-process-web
        command: ["/startup.sh", "biomaj_daemon_consumer.py"]

    biomaj-watcher-web:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - WAIT_HOSTS=biomaj-redis:6379, biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-user-web
            - biomaj-daemon-web
            - biomaj-elasticsearch
        command: ["/startup.sh", "gunicorn", "-c", "/etc/biomaj/gunicorn_conf.py", "-b", "0.0.0.0:5000", "--log-config", "/etc/biomaj/production.ini --paste /etc/biomaj/production.ini biomajwatcher.biomajwatcher:main"]

    biomaj-cron:
        image: quay.io/genouest/biomaj-cron
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
        depends_on:
            - biomaj-daemon-web

    biomaj-ftp:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajftp
            - RABBITMQ_USER=biomaj
            - RABBITMQ_PASSWORD=biomaj
            - MASQUERADE_ADDRESS=${MASQUERADE_ADDRESS}
            - WAIT_HOSTS=biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-mongo
            - biomaj-consul
            - biomaj-user-web
            - biomaj-elasticsearch
        ports:
            - "2121:21"
        command: ["/startup.sh", "biomaj_ftp_service.py"]

    biomaj-release-web:
        image: quay.io/genouest/biomaj
        build:
            context: .
        volumes:
            - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
        environment:
            - BIOMAJ_CONFIG=/etc/biomaj/config.yml
            - REDIS_PREFIX=biomajrelease
            - REDIS_DAEMON_PREFIX=biomajdaemon
            - WAIT_HOSTS=biomaj-redis:6379, biomaj-mongo:27017, biomaj-consul:8500
        depends_on:
            - biomaj-consul
            - biomaj-redis
            - biomaj-daemon-web
            - biomaj-daemon-message
        command: ["/startup.sh", "biomaj_release.py"]

    biomaj-expose:
        image: quay.io/genouest/biomaj-expose
        labels:
            - traefik.enable=true
            - traefik.frontend.rule=PathPrefix:/db
            - traefik.frontend.auth.forward.address=http://biomaj-daemon-web:5000/api/daemon/expose
            - traefik.frontend.auth.forward.trustForwardHeader=true
        depends_on:
            - biomaj-internal-proxy
        build:
            context: proxy/nginx
        volumes:
            - ./proxy/nginx/default.conf:/etc/nginx/conf.d/default.conf:ro
            - ${BIOMAJ_DIR}/biomaj/db:/db:ro
        command: [nginx-debug, '-g', 'daemon off;']