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Docker Guide

Included in this repo are the tools to run a containerized Opentrons robot stack in docker.

This includes the robot-server connected to the hardware emulation application. The emulation application includes the Smoothie and magnetic, temperature, and thermocycler modules.

Requirements

How to use

Start a terminal and change directory to the root of this repo.

  1. Build Enter docker-compose build --force-rm at the terminal.
  2. Run Enter docker-compose up at the terminal. The build and run stages can be combined docker-compose up --build.
  3. Start the Opentrons application.
  4. Click MORE on the bottom left. Then select NETWORK & SYSTEM. Click MANAGE and add 127.0.0.1 to the Manually Add Robot Network Address dialog.
  5. The docker container will appear as dev. Connect and run just as you would on a robot.

Configuration

Pipettes

By default a p20_multi_v2.0 is on the left mount and p20_single_v2.0 is on the right. These can be changed by modifying environment variables in the docker-compose.yml file.

Under the emulator section add an environment section with a variable called OT_EMULATOR_smoothie. A stringified JSON object with model and id field for the left and right mounts is defined by OT_EMULATOR_smoothie. All fields are optional.

For example to use a p300_multi on the right add:

  environment:
    OT_EMULATOR_smoothie: '{"right": {"model": "p300_multi"}}'

Adding more emulators

Magdeck

To add a second mag deck emulator make a copy of the existing magdeck section and change the key and serial_number.

For example this adds a magdeck with the serial number magdeck2:

 magdeck2:
    build: .
    command: python3 -m opentrons.hardware_control.emulation.scripts.run_module_emulator magdeck emulator
    links:
      - 'emulator'
    depends_on:
      - 'emulator'
    environment:
      OT_EMULATOR_magdeck: '{"serial_number": "magdeck2", "model":"mag_deck_v20", "version":"2.0.0"}'

Tempdeck

To add a second temp deck emulator make a copy of the existing tempdeck section and change the key and serial_number.

For example this adds a tempdeck with the serial number tempdeck2:

 tempdeck2:
    build: .
    command: python3 -m opentrons.hardware_control.emulation.scripts.run_module_emulator tempdeck emulator
    links:
      - 'emulator'
    depends_on:
      - 'emulator'
    environment:
      OT_EMULATOR_tempdeck: '{"serial_number": "tempdeck2", "model":"temp_deck_v20", "version":"v2.0.1", "temperature": {"starting":0.0, "degrees_per_tick": 2.0}}'

Thermocycler

To add a second thermocycler emulator make a copy of the existing thermocycler section and change the key and serial_number.

For example this adds a thermocycler with the serial number thermocycler2:

 thermocycler2:
    build: .
    command: python3 -m opentrons.hardware_control.emulation.scripts.run_module_emulator thermocycler emulator
    links:
      - 'emulator'
    depends_on:
      - 'emulator'
    environment:
      OT_EMULATOR_thermocycler: '{"serial_number": "thermocycler2", "model":"v02", "version":"v1.1.0", "lid_temperature": {"starting":23.0, "degrees_per_tick": 2.0},  "plate_temperature": {"starting":23.0, "degrees_per_tick": 2.0}}'

Known Issues

  • Pipettes cannot be changed at run time.