deployment/docker-compose.yml at master · bmeg/deployment · GitHub

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version: '3.4'
services:

  mongo:
    image: mongo:3.6
    restart: unless-stopped
    container_name: mongo
    volumes:
       - /mnt/data1/bmeg/mongo-data:/data/db

  grip:
    image: bmeg/grip:0.7.1
    restart: unless-stopped
    # build: grip
    container_name: grip
    volumes:
        - ./secrets/grip_config.yml:/config/grip_config.yml
    entrypoint: ["grip", "server", "--config", "/config/grip_config.yml"]
    ports:
      - 8201:8201
      - 8202:8202
    depends_on:
      - mongo

  nginx:
    build: nginx
    restart: unless-stopped
    container_name: nginx
    # use env_file to overwrite env values
    # see GRIP_SERVER
    env_file:
      - secrets/nginx.env
    ports:
      - 80:80
      - 443:443
    volumes:
      # content
      - /mnt/data2/bmeg/deployment/nginx/bmeg-site/bmegio.ohsu.edu/public:/usr/share/nginx/bmegio.ohsu.edu
      - /mnt/data2/bmeg/deployment/nginx/bmeg-site/bmeg.io/public:/usr/share/nginx/bmeg.io
      - /mnt/data2/bmeg/deployment/nginx/usr/share/nginx/gen3-ohsu.ddns.net:/usr/share/nginx/gen3-ohsu.ddns.net
      - /mnt/data2/bmeg/bmeg-data:/usr/share/nginx/bmegio.ohsu.edu.data
      - /mnt/data2/bmeg/bmeg-data:/usr/share/nginx/bmeg.io.data
      - /mnt/data2/bmeg/bmeg-share:/usr/share/nginx/bmegio.ohsu.edu.share
      - /mnt/data2/bmeg/bmeg-share:/usr/share/nginx/bmeg.io.share
      - /mnt/data2/recount/data:/usr/share/nginx/recount.bio.data
      - /mnt/data2/bmeg/deployment/nginx/usr/share/nginx/recount.bio:/usr/share/nginx/recount.bio

      # config
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/nginx.conf:/etc/nginx/nginx.conf
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/http.conf.d/env.conf:/etc/nginx/http.conf.d/env.conf
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/conf.d/default.conf:/etc/nginx/conf.d/default.conf
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/protected.conf:/etc/nginx/protected.conf
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/grip-bmeg.io.conf:/etc/nginx/grip-bmeg.io.conf
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/grip-bmegio.ohsu.edu.conf:/etc/nginx/grip-bmegio.ohsu.edu.conf
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/lua/nginx-google-oauth/access.lua:/etc/nginx/lua/nginx-google-oauth/access.lua

      # specific sites
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/bmegio.ohsu.edu:/etc/nginx/sites-enabled/bmegio.ohsu.edu:ro
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/gen3-ohsu.ddns.net:/etc/nginx/sites-enabled/gen3-ohsu.ddns.net:ro
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/bmeg-jupyter.ddns.net:/etc/nginx/sites-enabled/bmeg-jupyter.ddns.net:ro
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/bmeg.io:/etc/nginx/sites-enabled/bmeg.io:ro
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/recount.bio:/etc/nginx/sites-enabled/recount.bio:ro
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/methylation.recount.bio:/etc/nginx/sites-enabled/methylation.recount.bio:ro

      # testing
      - /mnt/data2/bmeg/deployment/nginx/etc/nginx/sites-enabled/commons.bmeg.io:/etc/nginx/sites-enabled/commons.bmeg.io:ro
      # - ./nginx/etc/nginx/sites-enabled/bmegio-test.ddns.net:/etc/nginx/sites-enabled/bmegio-test.ddns.net:ro
      # - ./nginx/bmeg-site/bmegio-test.ddns.net/public:/usr/share/nginx/bmegio-test.ddns.net
      # - ./nginx/etc/nginx/grip-bmegio-test.ddns.net.conf:/etc/nginx/grip-bmegio-test.ddns.net.conf

      # for letsencrypt
      - /mnt/data2/bmeg/deployment/data/certbot/conf:/etc/letsencrypt
      - /mnt/data2/bmeg/deployment/data/certbot/www:/var/www/certbot

      # startup
      - /mnt/data2/bmeg/deployment/nginx/run.sh:/etc/nginx/run.sh

    depends_on:
      - grip
      - jupyterhub
      - cadvisor


  # for letsencrypt
  certbot:
    image: certbot/certbot
    restart: unless-stopped
    container_name: certbot
    volumes:
      - ./data/certbot/conf:/etc/letsencrypt
      - ./data/certbot/www:/var/www/certbot
    entrypoint: "/bin/sh -c 'trap exit TERM; while :; do certbot renew; sleep 12h & wait $${!}; done;'"

  # python & go container for loading data, running tests, etc.
  etl:
    build: etl
    restart: unless-stopped
    container_name: etl
    volumes:
      # mount bmeg-etl directory, to have access to `outputs/`
      - /mnt/data2/bmeg/bmeg-data/:/etl/bmeg-data
      # mount bmeg-etl
      - /mnt/data2/bmeg/bmeg-etl:/etl/bmeg-etl
    depends_on:
      - grip
      - mongo

  # see https://opendreamkit.org/2018/10/17/jupyterhub-docker/
  jupyterhub:
    build: jupyterhub                # Build the container from this folder.
    restart: unless-stopped
    container_name: jupyterhub       # The service will use this container name.
    volumes:                         # Give access to Docker socket.
      - /var/run/docker.sock:/var/run/docker.sock
      - ./secrets/userlist:/srv/jupyterhub/userlist
      - ./secrets/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py
      - /mnt/data1/bmeg/jupyter-data:/data
    environment:                     # Env variables passed to the Hub process.
      DOCKER_NOTEBOOK_IMAGE: jupyterlab_img
      DOCKER_NETWORK_NAME: deployment_default
      HUB_IP: jupyterhub
    env_file:
      - secrets/jupyter.env
      - secrets/oauth.env
    depends_on:
      - grip

  # notebook image, build via: `dc build jupyterlab`
  # The extra line command: echo is there so that,
  # when Docker Compose starts the service, it terminates immediately.
  # Indeed this image is meant to be loaded by the Hub, not by Compose.
  jupyterlab:
    build: jupyterlab
    image: jupyterlab_img
    restart: unless-stopped
    command: echo


  # see https://www.neteye-blog.com/2018/04/how-to-monitor-docker-containers-using-cadvisor-part-1/
  cadvisor:
    container_name: cadvisor       # The service will use this container name.
    image: google/cadvisor:latest
    restart: unless-stopped
    volumes:
    - /:/rootfs:ro
    - /var/run:/var/run:rw
    - /sys:/sys:ro
    - /var/lib/docker/:/var/lib/docker:ro
    ports:
      - 8080:9090

#
# # docker volume create --name=jupyterhub-data
# # docker volume create --name=jupyterhub-db-data
# volumes:
#   data:
#     external:
#       name: ${DATA_VOLUME_HOST}
#   db:
#     external:
#       name: ${DB_VOLUME_HOST}

# networks:
#   default:
#     external:
#       name: ${DOCKER_NETWORK_NAME}