docker-compose.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
    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:gcloud-prod
    environment:
      # Fetched using `gsutil cp gs://hail-common/references/grch37_to_grch38.over.chain.gz /liftOver/` inside container
      - GRCH37_TO_GRCH38_LIFTOVER_REF_PATH=/liftOver/grch37_to_grch38.over.chain.gz
      # Fetched using `gsutil cp gs://hail-common/references/grch38_to_grch37.over.chain.gz /liftOver/` inside container
      - GRCH38_TO_GRCH37_LIFTOVER_REF_PATH=/liftOver/grch38_to_grch37.over.chain.gz
    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
      # Stores liftover chain files mentioned above
      - ./liftOver:/liftOver
    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