Introduction

This session aims to introduce the use of Docker containers with the goal of using them to effect reproducible computational environments. Such environments are useful for ensuring reproducible research outputs, for example.

The practical work in this lesson is primarily aimed at using Docker on your own laptop. Beyond your laptop, software container technologies such as Docker can also be used in the cloud and on high performance computing (HPC) systems. Some of the material in this lesson will be applicable to those environments too.

Learning Objectives

By the end of this workshop, you will know how to:

  • Have an understanding of what Docker containers are, why they are useful and the common terminology used
  • Have a working Docker installation on your local system to allow you to use containers
  • Understand how to use existing Docker containers for common tasks
  • Be able to build your own Docker containers by understanding both the role of a Dockerfile in building containers, and the syntax used in Dockerfiles
  • Understand how to manage Docker containers on your local system
  • Appreciate issues around reproducibility in software, understand how containers can address some of these issues and what the limits to reproducibility using containers are

Course Outline

Time Lesson Questions
20 Introducing Containers What are containers, and why might they be useful to me?
10 Introducing the Docker Command Line How do I know Docker is installed and running?
How do I interact with Docker?
20 Exploring and Running Containers How do I interact with Docker containers and container images on my computer?
10 Cleaning Up Containers How do I interact with a Docker container on my computer?
How do I manage my containers and container images?
10 Finding Containers on Docker Hub What is the Docker Hub, and why is it useful?
20 Creating Your Own Container Images How can I make my own Docker container images?
How do I document the ‘recipe’ for a Docker container image?
30 Creating More Complex Container Images How can I add local files (e.g. data files) into container images at build time?
How can I access files stored on the host system from within a running Docker container?
10 Examples of Using Container Images in Practice How can I use Docker for my own work?
20 Containers in Research Workflows: Reproducibility and Granularity How can I use container images to make my research more reproducible?
How do I incorporate containers into my research workflow?

Prerequisites

  • You should have basic familiarity with using a command shell, and the lesson text will at times request that you “open a shell window”, with an assumption that you know what this means.
    • Under Linux or macOS it is assumed that you will access a bash shell (usually the default), using your Terminal application.
    • Under Windows, Powershell and Git Bash should allow you to use the Unix instructions. We will also try to give command variants for Windows cmd.exe.
  • The lessons will sometimes request that you use a text editor to create or edit files in particular directories. It is assumed that you either have an editor that you know how to use that runs within the working directory of your shell window (e.g. nano), or that if you use a graphical editor, that you can use it to read and write files into the working directory of your shell.

Website accounts to create

Please seek help at the start of the lesson if you have not been able to establish a website account on:

  • The Docker Hub. We will use the Docker Hub to download pre-built container images, and for you to upload and download container images that you create, as explained in the relevant lesson episodes.

Files to download

Download the docker-intro.zip file. Move the downloaded file to your Desktop and unzip it. It should unzip to a folder called docker-intro.

Software to install

Docker’s installation experience has steadily improved, however situations will arise in which installing Docker on your computer may not be straightforward unless you have a large amount of technical experience. Workshops try to have helpers on hand that have worked their way through the install process, but do be prepared for some troubleshooting.

In most cases, you will need to have administrator rights on the computer in order to install the Docker software. If you are using a computer managed by your organisation and do not have administrator rights, you may be able to get your organisation’s IT staff to install Docker for you. Alternatively your IT support staff may be able to give you remote access to a server that can run Docker commands.

Please try to install the appropriate software from the list below depending on the operating system that your computer is running. Do let the workshop organisers know as early as possible if you are unable to install Docker using these instructions, as there may be other options available.

Microsoft Windows

You must have admin rights to run Docker! Some parts of the lesson will work without running as admin but if you are unable to Run as administrator on your machine some elements of this workshop might not work as described.

Ideally, you will be able to install the Docker Desktop software, following the Docker website’s documentation. Note that the instructions for installing Docker Desktop on Windows 10 Home Edition are different from other versions of Windows 10.

Note that the above installation instructions highlight a minimum version or “build” that is required to be able to install Docker on your Windows 10 system. See Which version of Windows operating system am I running? for details of how to find out which version/build of Windows 10 you have.

If you are unable to follow the above instructions to install Docker Desktop on your Windows system, the final release of the deprecated Docker Toolbox version of Docker for Windows can be downloaded from the releases page of the Docker Toolbox GitHub repository. (Download the .exe file for the Windows installer). Please note that this final release of Docker Toolbox includes an old version of Docker and you are strongly advised not to attempt to use this for any production use. It will, however, enable you to follow along with the lesson material.

Warning: Git Bash

If you are using Git Bash as your terminal on Windows then you should be aware that you may run into issues running some of the commands in this lesson as Git Bash will automatically re-write any paths you specify at the command line into Windows versions of the paths and this will confuse the Docker container you are trying to use. For example, if you enter the command:

docker run alpine cat /etc/os-release

Git Bash will change the /etc/os-release path to C:\etc\os-release\ before passing the command to the Docker container and the container will report an error. If you want to use Git Bash then you can request that this path translation does not take place by adding an extra / to the start of the path. i.e. the command would become:

docker run alpine cat //etc/os-release

This should suppress the path translation functionality in Git Bash.

Apple macOS

Ideally, you will be able to install the Docker Desktop software, following the Docker website’s documentation. The current version of the Docker Desktop software requires macOS version 10.14 (Mojave) or later.

If you already use Homebrew or MacPorts to manage your software, and would prefer to use those tools rather than Docker’s installer, you can do so. For Homebrew, you can run the command brew install --cask docker. Note that you still need to run the Docker graphical user interface once to complete the initial setup, after which time the command line functionality of Docker will become available. The Homebrew install of Docker also requires a minimum macOS version of 10.14. The MacPorts Docker port should support older, as well as the most recent, operating system versions (see the port details), but note that we have not recently tested the Docker installation process via MacPorts.

Linux

There are too many varieties of Linux to give precise instructions here, but hopefully you can locate documentation for getting Docker installed on your Linux distribution. It may already be installed. If it is not already installed on your system, the Install Docker Engine page provides an overview of supported Linux distributions and pointers to relevant installation information. Alternatively, see:

Verify Installation

To quickly check if the Docker and client and server are working run the following command in a new terminal or ssh session:

$ docker version
Client:
 Version:           20.10.2
 API version:       1.41
 Go version:        go1.13.8
 Git commit:        20.10.2-0ubuntu2
 Built:             Tue Mar  2 05:52:27 2021
 OS/Arch:           linux/arm64
 Context:           default
 Experimental:      true

Server:
 Engine:
  Version:          20.10.2
  API version:      1.41 (minimum version 1.12)
  Go version:       go1.13.8
  Git commit:       20.10.2-0ubuntu2
  Built:            Tue Mar  2 05:45:16 2021
  OS/Arch:          linux/arm64
  Experimental:     false
 containerd:
  Version:          1.4.4-0ubuntu1
  GitCommit:        
 runc:
  Version:          1.0.0~rc95-0ubuntu1~21.04.1
  GitCommit:        
 docker-init:
  Version:          0.19.0
  GitCommit:

The above output shows a successful installation and will vary based on your system. The important part is that the “Client” and the “Server” parts are both working and returns information. It is beyond the scope of this document to debug installation problems but common errors include the user not belonging to the docker group and forgetting to start a new terminal or ssh session.

A quick tutorial on copy/pasting file contents from episodes of the lesson

Let’s say you want to copy text off the lesson website and paste it into a file named myfile in the current working directory of a shell window. This can be achieved in many ways, depending on your computer’s operating system, but routes I have found work for me:

  • macOS and Linux: you are likely to have the nano editor installed, which provides you with a very straightforward way to create such a file, just run nano myfile, then paste text into the shell window, and press control+x to exit: you will be prompted whether you want to save changes to the file, and you can type y to say “yes”.
  • Microsoft Windows running cmd.exe shells:
    • del myfile to remove myfile if it already existed;
    • copy con myfile to mean what’s typed in your shell window is copied into myfile;
    • paste the text you want within myfile into the shell window;
    • type control+z and then press enter to finish copying content into myfile and return to your shell;
    • you can run the command type myfile to check the content of that file, as a double-check.
  • Microsoft Windows running PowerShell:

    • The cmd.exe method probably works, but another is to paste your file contents into a so-called “here-string” between @' and '@ as in this example that follows (the “>” is the prompt indicator):

      > @'
Some hypothetical
file content that is

split over many

lines.
'@ | Set-Content myfile -encoding ascii

Credits and Acknowledgement

These content were adapted from the following course materials: