anyvar/compose.yaml at main · biocommons/anyvar · GitHub

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services:

  # If you have a SeqRepo database already on your local filesystem,
  # you can comment this `seqrepo` container out and replace `seqrepo_vol`
  # everywhere in this file with that path, or read the path from a variable
  # like SEQREPO_ROOT_DIR.
  # e.g. under the `anyvar` container, replace
  # volumes:
  #   - seqrepo_vol:/usr/local/share/seqrepo
  #
  # with
  #
  # volumes:
  #   - $SEQREPO_ROOT_DIR:/usr/local/share/seqrepo
  seqrepo:
    image: biocommons/seqrepo:2024-12-20
    volumes:
      - seqrepo_vol:/usr/local/share/seqrepo

  # This can also be used in place of the `seqrepo` container if you have
  # an existing SeqRepo database on your local filesystem and want to copy it
  # to a docker volume.
  # Export SEQREPO_ROOT_DIR for the compose command
  # e.g. SEQREPO_ROOT_DIR=/my/seqrepo docker-compose up
  # If using this container, make sure you have commented out the `seqrepo` container
  # and changed the `depends_on` for the `anyvar` container to depend on  `seqrepo_local_populator` instead of `seqrepo`.
  # seqrepo_local_populator:
  #   # image: alpine
  #   image: eeacms/rsync
  #   volumes:
  #     - seqrepo_vol:/usr/local/share/seqrepo
  #     - $SEQREPO_ROOT_DIR:/seqrepo:ro
  #   command: >
  #     /bin/sh -c "rsync -a --delete /seqrepo/2024-12-20/ /usr/local/share/seqrepo/2024-12-20/"

  uta:
    # Test:
    # psql -XAt postgres://anonymous@localhost:5433/uta -c 'select count(*) from uta_20241220.transcript'
    # 329090
    image: biocommons/uta:uta_20241220
    environment:
      - POSTGRES_PASSWORD=some-password-that-you-make-up
    volumes:
      - uta_vol:/var/lib/postgresql/data
      - type: bind
        source: ./uta_20241220.pgd.gz
        target: /tmp/uta_20241220.pgd.gz
        read_only: true
        bind:
          create_host_path: false
    ports:
      - 127.0.0.1:5433:5432

  anyvar_db:
    image: postgres:17
    volumes:
      - anyvar_vol:/var/lib/postgresql/data
    ports:
      - 127.0.0.1:5434:5432
    environment:
      - POSTGRES_DB=anyvar
      - POSTGRES_USER=anyvar
      - POSTGRES_PASSWORD=anyvar-pw

  anyvar:
    image: docker.io/clingendevs/anyvar:latest
    volumes:
      - seqrepo_vol:/usr/local/share/seqrepo
    depends_on:
      anyvar_db:
        required: true
        condition: service_started
      seqrepo:
        required: true
        condition: service_completed_successfully
    environment:
      - SEQREPO_INSTANCE_DIR=/usr/local/share/seqrepo/2024-12-20
      - SEQREPO_DATAPROXY_URI=seqrepo+file:///usr/local/share/seqrepo/2024-12-20
      - UTA_DB_URL=postgresql://anonymous:anonymous@uta:5432/uta/uta_20241220
      - ANYVAR_STORAGE_URI=postgresql://anyvar:anyvar-pw@anyvar_db:5432/anyvar
    ports:
      - 127.0.0.1:8010:8000

volumes:
  seqrepo_vol:
    external: true
  uta_vol:
    external: true
  anyvar_vol:
    external: true