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Docker is a tool that is designed to make it easier to create and run applications by using containers. A container is a virtual environment that allows a developer to package an application with all of the necessary ingredients (requirements) for it to run, and bundles it up into one portable package. While simple in concept, this is a very powerful tool that allows you to create computing environments that can be replicated on most modern computers. Here are a few example use cases for a scientist:

  • A sharable computing environment so that all members of your lab have access to the same tools
  • An easily replicable experiment that can be run from anywhere.
  • An analysis pipeline with all of the necessary code to replicate figures and statistics from a published paper.
  • An application that runs Jupyter server so that you can access the same data and software without installing anything locally.

Getting Started at MIND:

  • Follow Eshin's instructions in the README found here

Getting Started on you own:

  • Install Docker and Google Chrome

  • Follow the instructions in Dockerfile_example. This file serves as a set of instructions for building a docker image. Best practices in writing a Dockerfile can be found here.

  • To build the docker image, make sure you have docker running, navigate to the directory that contains your Dockerfile and execute the line: docker build -t cdl .. This will create a docker image from the instructions you specified in Dockerfile.

  • Once the docker image builds, you can launch it by executing the following command: docker run -it -p 9999:9999 --name CDL -v ~/Desktop:/mnt cdl. To unpack this, run runs the image. -it starts the container as an interactive process (like a shell). -p opens and links a port on the docker to a port on your local computer. --name names the container. -v allows you to share a volume between the docker container and your local computer. cdl at the end specifies which image you want to run. For more details on docker run, see this link. You should now see the root@ prefix in your terminal, if so you've successfully created a container and are running a shell from inside!

  • Launch the demo jupyter notebook: jupyter notebook demo.ipynb --port=9999 --no-browser --ip= --allow-root and then navigate to localhost:9999 (+ a token) in your browser to access the notebook.

Helpful commands

  • See what docker images you have downloaded and can be used to create new containers:
    • docker images
  • See running container dockers:
    • docker ps
  • See all docker containers you have created (including those not running):
    • docker ps -a
  • Startup and connect to previously created container:
    • docker start yourContainerName
    • docker attach yourContainerName
  • Delete a docker container:
    • docker rm yourContainerName
  • Delete a docker image:
    • docker rmi yourImageName
  • Stop a running container:
    • docker stop yourContainerName
  • Execute a new command in an existing docker container
    • docker exec yourContainer command
  • Delete all containers that are no longer running:
    • docker rm $(docker ps -aq -f status=exited)
  • Force delete ALL containers
    • docker rm -f $(docker ps -aq)
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