docker-compose.dev.yml

version: '2.4'

services:
  postgres:
    image: postgres:12.6
    command: postgres -c listen_addresses='*'
    environment:
      - PGPORT=5433
      - POSTGRES_PASSWORD=docker-compose-postgres-password
    volumes:
      - ./data/postgres:/var/lib/postgresql/data
    healthcheck:
      test: pg_isready -h postgres -U postgres
      interval: 5s
      timeout: 10s
      retries: 100

  redis:
    image: gcr.io/seqr-project/redis:gcloud-prod
    healthcheck:
      test: redis-cli ping
      interval: 3s
      timeout: 5s
      retries: 100

  # elasticsearch:
  #   image: docker.elastic.co/elasticsearch/elasticsearch:7.16.3
  #   volumes:
  #     - /mnt/hpf/data/elasticsearch:/usr/share/elasticsearch/data
  #   container_name: elasticsearch
  #   environment:
  #     - http.host=0.0.0.0
  #     - discovery.type=single-node
  #     - cluster.routing.allocation.disk.threshold_enabled=false
  #   healthcheck:
  #     test: bash -c "curl -s elasticsearch:9200/_cat/health | grep green"
  #     interval: 3s
  #     timeout: 5s
  #     retries: 100
  #   ports:
  #     - 9200:9200

#  kibana:
#    image: docker.elastic.co/kibana/kibana:7.16.3
#    environment:
#      - ELASTICSEARCH_HOSTS=http://elasticsearch:9200
#    depends_on:
#      elasticsearch:
#        condition: service_healthy
#    healthcheck:
#      test: bash -c "curl -s kibana:5601 | grep kibana"
#      interval: 3s
#      timeout: 5s
#      retries: 100

  seqr:
    build: .
    image: ccm-seqr:dev
    volumes:
      - /mnt/hpf/bam_files:/readviz
      # - ./data/readviz:/readviz
      - /mnt/hpf/data/seqr_static_files:/seqr_static_files
      - ./settings.py:/seqr/settings.py
      - ./gunicorn/gunicorn_config.py:/seqr/gunicorn_config.py
      - ./logs/django:/var/log/django
      - ./logs/gunicorn:/var/log/gunicorn
    ports:
      - 8000:8000
    develop:
      watch:
        - action: sync
          path: ./ui
          target: /seqr/ui
    environment:
      - BASE_URL=https://seqr.ccm.sickkids.ca
      - SEQR_GIT_BRANCH=dev
      - PYTHONPATH=/seqr
      - STATIC_MEDIA_DIR=/seqr_static_files
      - POSTGRES_SERVICE_HOSTNAME=postgres
      - POSTGRES_SERVICE_PORT=5433
      - POSTGRES_PASSWORD=docker-compose-postgres-password
      - ELASTICSEARCH_SERVICE_HOSTNAME=elasticsearch
      - REDIS_SERVICE_HOSTNAME=redis
      - KIBANA_SERVICE_HOSTNAME=kibana
      - PGHOST=postgres
      - PGPORT=5433
      - PGUSER=postgres
      - GUNICORN_WORKER_THREADS=4
      - ANALYST_USER_GROUP=analyst
    depends_on:
      postgres:
        condition: service_healthy
      # elasticsearch:
      #   condition: service_healthy
      redis:
        condition: service_healthy
    healthcheck:
      test: bash -c "curl -s 'http://localhost:8000' | grep html"

  # pipeline-runner:
  #   image: gcr.io/seqr-project/pipeline-runner:20220526_130649
  #   volumes:
  #     - /mnt/hpf/data/seqr-reference-data:/seqr-reference-data
  #     - /mnt/hpf/data/vep_data:/vep_data
  #     - /mnt/hpf/data/input_vcfs:/input_vcfs
  #     - ./pipeline_runner/download_reference_data.sh:/usr/local/bin/download_reference_data.sh
  #     - ./pipeline_runner/ensembl-vep-release-104:/ensembl-vep-release-104
  #     - ./pipeline_runner/entrypoint.sh:/entrypoint.sh
  #     - ./pipeline_runner/update_clinvar_matrix_table.sh:/usr/local/bin/update_clinvar_matrix_table.sh
  #     - ./pipeline_runner/update_combined_reference_data.sh:/usr/local/bin/update_combined_reference_data.sh
  #     - ./pipeline_runner/vep_configs/vep-GRCh37-loftee.json:/vep_configs/vep-GRCh37-loftee.json
  #     - ./pipeline_runner/vep_configs/vep-GRCh38-loftee.json:/vep_configs/vep-GRCh38-loftee.json
  #     - ~/.config:/root/.config
  #   depends_on:
  #     elasticsearch:
  #       condition: service_healthy

  # nginx:
  #   image: nginx
  #   ports:
  #     - 80:80
  #     - 443:443
  #   depends_on:
  #     seqr:
  #       condition: service_healthy
  #   volumes:
  #     - ./nginx/conf.d/default.conf:/etc/nginx/conf.d/default.conf
  #     - ./nginx/certs:/etc/nginx/certs
  #     - ./logs/nginx:/var/log/nginx