Environment Setup

Welcome to the workshop on deploying Opal and Molgenis Armadillo infrastructure using Docker. This guide will help you set up your environment to ensure a smooth experience during the workshop.

Prerequisites

Operating System

• Windows Users: Ensure you have WSL2 installed. This allows you to run a Linux environment directly on Windows, which is necessary for Docker.
• Mac and Linux Users: You are good to go with your native terminal.
• Reference System: This workshop material has been tested on Ubuntu 24.04.3 LTS

Software Requirements

1. Docker Engine (>= 28.3.3) with Docker Compose
   • Windows/macOS: Docker Desktop bundles Docker Compose.
   • Linux: Install Docker Engine and Docker Compose separately.
   • Required version: Docker Compose v2.39.2 or later
2. Git (>= 2.43.0)
   • Used for cloning workshop repositories and version control
   • Download from git-scm.com
   • Alternative: GitHub Desktop for a graphical interface
   • Verify installation: git --version
3. Terminal or shell (PowerShell, Windows Terminal, macOS Terminal, Linux shell)
4. Text Editor/IDE: VS Code, Sublime, Vim, or similar.
5. R (>= 4.3.3) and RStudio Desktop (optional but recommended for client-side checks)

Hardware requirements

• At least 4 CPU cores and 8 GB RAM recommended (4 GB minimum)
• 10+ GB free disk space for images, containers, and volumes

Network and permissions

• Administrative rights to install software
• Unrestricted internet access to docker.io, ghcr.io and GitHub
• VPN/proxy configured for Docker if required by your organization
• Virtualization enabled in BIOS/UEFI (Intel VT-x/AMD-V or Apple virtualization)

Install Docker

Windows (WSL2)

• Install and enable WSL2: Microsoft guide
• Install Docker Desktop: Docker Desktop for Windows
• In Docker Desktop settings, enable “Use the WSL 2 based engine” and integration with your WSL distro

macOS

• Install Docker Desktop: Docker Desktop for Mac

Linux

• Install Docker Engine following the official docs: Install Docker Engine
• Install Docker Compose (standalone): Install Docker Compose

Linux post-install (non-root usage)

# Add your user to the docker group and activate it
sudo usermod -aG docker $USER
# Restart your terminal to activate the changes

Verify your setup

Run the following commands. All should succeed without errors.

docker --version
docker-compose --version
docker run --rm hello-world

Expected output (or newer versions):

Docker version 28.3.3, build 980b856 Docker Compose version v2.39.2-desktop.1

Expected output (or newer versions):

Docker version 28.3.3, build 980b856
Docker Compose version v2.39.2-desktop.1

Additional Notes

• Ensure your Docker engine is allocated with sufficient memory (at least 4GB; 8GB recommended) to avoid performance issues.
• Close applications using typical service ports you plan to map (e.g., 8080, 8443) to avoid conflicts.
• On corporate networks, confirm Docker can pull images from public registries.
• Familiarize yourself with basic Docker commands and docker-compose operations, as we will be interacting with the console during the workshop.
• Important: We use docker-compose (with hyphen) throughout this workshop, not docker compose (space-separated).

Learn Docker: quick references

• Docker Getting Started: docs.docker.com/get-started
• Docker CLI reference: docs.docker.com/engine/reference/commandline/docker
• Docker Compose overview: docs.docker.com/compose
• Volumes and persistence: docs.docker.com/storage/volumes
• Play with Docker (hands-on labs): labs.play-with-docker.com

By following these steps, your environment will be ready for the workshop. If you encounter any issues, feel free to reach out to the workshop organizers for assistance.