Precourse instructions

Background knowledge: UNIX

As stated in the course prerequisites at the announcement web page, we expect participants to have a basic understanding of working with the command line on UNIX-based systems. You can test your UNIX skills with a quiz here. If you don’t have experience with UNIX command line, or if you’re unsure whether you meet the prerequisites, follow our online UNIX tutorial.

Software

OS and terminal

During the course exercises you will be mainly interacting with Docker through the command line. If you are using a UNIX or UNIX-like OS (e.g MacOS), you already have a terminal readily usable for the course. If you are working with Windows, although Windows Powershell is suitable for that, we strongly recommend to install a UNIX or ‘UNIX-like’ terminal. You can get this by using MobaXterm or WSL2 (recommended solution).

Code editor

You should have a modern code editor installed. During the course, we can give only limited help for installation and set-up issues, so we will only “officially” support VS Code. If you are already very familiar with another combination of modern code editor/command line interface, feel free to use it, but know that support for this will be limited.

Docker

You will need to create a Docker Hub account and install Docker on your local computer. This will allow you to build and push Docker images to Docker Hub, which is required for some of the exercises. You will also need Docker to run some of the exercises locally.

Docker Hub account creation

You can create an account here. For this course, we recommend to create a personal account.

Docker CLI installation

The Docker CLI (docker) is the command-line tool used to interact with Docker daemons and manage containers, images, networks, and volumes.

Docker can be installed in two main ways:

• Docker Desktop: An all-in-one application for macOS and Windows that includes the Docker CLI, Docker Engine, a graphical interface, and additional developer tools
• Docker Engine: The container runtime itself. On Linux, Docker Engine and the Docker CLI are typically installed directly from the distribution packages or Docker repositories

For this course, you need to install:

• Docker Engine on Linux
• Docker Desktop on macOS and Windows

Linux

Install Docker Engine by following the official instructions for your Linux distribution. The installation will include both Docker Engine and the Docker CLI.

macOS

Install Docker Desktop by following the official instructions for MacOS. Docker Desktop includes the Docker CLI and makes it available in the terminal.

Windows

Install Docker Desktop by following the official instructions for Windows. Docker Desktop includes the Docker CLI and makes it available for use in PowerShell, Command Prompt, and Windows Terminal.

Verify the installation

Open a terminal and run:

docker --version

You should see an output similar to:

Docker version 29.5.2, build 79eb04c

You can also verify that the Docker daemon is reachable by running:

docker info

If Docker is correctly installed and running, information about the Docker server and client will be displayed:

Client: Docker Engine - Community
 Version:    29.5.2
 Context:    default
 Debug Mode: false
 Plugins:
  buildx: Docker Buildx (Docker Inc.)
    Version:  v0.34.1
    Path:     /usr/libexec/docker/cli-plugins/docker-buildx
  compose: Docker Compose (Docker Inc.)
    Version:  v5.1.4
    Path:     /usr/libexec/docker/cli-plugins/docker-compose
...

Apptainer

You don’t need to install Apptainer on your local machine as you will be using a version we installed on the remote server. However, if you want to have a look before the course, you can find installation instructions for different OS here. We recommend the non-setuid install.

SSH connection to a server

In addition to your local computer, you will be working on an Amazon Web Services (AWS) Elastic Cloud (EC2) server. This Ubuntu server behaves like a ‘normal’ remote server, and can be approached through ssh. If you are enrolled in the course, you have access to a shared document containing instruction to retrieve your username and private ssh key, granting you access to a personal home directory on the server.

VS Code instructions

Here are instructions on how to use VS Code to connect with SSH to a remote server. First, place the key_username.pem file in the proper folder:

Move-Item -Path key_username.pem -Destination $HOME\.ssh

chmod 400 key_username.pem
mv key_username.pem ~/.ssh

Then:

• Open VS Code and click on the button with the >< icon in the bottom left corner
• Select Connect to Host... and then Configure SSH Hosts...
• Specify a location for the SSH config file (preferably the same directory as where your keys are stored): ~/.ssh/config

• A skeleton config file will be provided. Edit it, so it looks like this (replace username with your username, and make sure the IP address in HostName match what the one given in the shared document):

  WindowsMacOS/Linux

  Host sib_course_remote
      User username
      HostName 52.57.40.7
      IdentityFile ~\.ssh\key_username.pem
  

  Note: if you are working with the Windows SSH executable (for example C:\WINDOWS\System32\OpenSSH\ssh.exe), you may have to use the full path of the key file instead of a relative one in IdentityFile:

      IdentityFile C:\Users\<windows_username>\.ssh\key_username.pem
  

  Host sib_course_remote
      User username
      HostName 52.57.40.7
      IdentityFile ~/.ssh/key_username.pem
  

Finally:

• Save and close the config file
• Click again on the >< button in the bottom left corner
• Select Connect to Host..., and then sib_course_remote. You will be asked which operating system is used on the remote. Choose Linux

Video tutorial

You can find below a video tutorial showing how to configure SSH connections in VS Code:

ssh -i key_username.pem username@52.57.40.7