Last updated: 2019-01-28

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Rmd 86f5c3d John Blischak 2019-01-28 Add notes on using Docker.

Docker is virtualization software. The official documentation is at docs.docker.com.

Terminology:

Getting help:

docker --help
docker <subcommand> --help

Using Docker containers

The name of an image is referred to as a repository. If the repository is from a remote source like DockerHub, it will also have an associated username. Lastly, each version of the image has a specific tag (the default is latest). Thus in the commands below, any instance of <image> can be replaced with the corresponding (username/)repository(:tag) that specifies the desired image.

docker pull <image>
docker pull continuumio/miniconda3
docker pull continuumio/miniconda3:4.5.11
docker image ls
# Alternative:
docker images
docker run --rm <image> <command>
docker container ls
# Alternative:
docker ps
docker stop <container>

You can reference the container by its ID or Name (you have to run docker container ls to obtain this information).

docker run --rm -it <image>
# Depending on the Dockerfile, you may have to specify the executable to run
docker run --rm -it <image> bash

Building a Docker image

docker build -t <name-of-tag> .
# Remove exited containers:
docker ps -aq --no-trunc -f status=exited | xargs docker rm
# Remove untagged images:
docker images -q --filter dangling=true | xargs docker rmi
# Start with the xenial tag of the ubuntu image
FROM ubuntu:xenial

# Add contact info
MAINTAINER <name>, <email>

# Install software
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    emacs \
    git \
    nano

# Execute code
RUN mkdir /root/project

# Set the working directory
WORKDIR /root/project

# Copy file from local machine to Docker image
COPY file.txt /root/project/

# Copy directory from local machine to Docker image
COPY dir/ /root/project/dir/

# Run this command by default when running an interactive container
CMD [ "/bin/bash" ]

Useful images

Launch Jupyter from a Docker container (see my comment on GitHub for details):

docker run -i -t -p 8888:8888 continuumio/miniconda3 /bin/bash -c "/opt/conda/bin/conda install -c conda-forge jupyter -y --quiet && mkdir /opt/notebooks && /opt/conda/bin/jupyter notebook --notebook-dir=/opt/notebooks --ip='0.0.0.0' --port=8888 --no-browser --allow-root"