Prerequisites

Before installing Parthenon, ensure your system meets these requirements. Parthenon runs entirely in Docker containers, so the host requirements are minimal.

Hardware Requirements

Component	Minimum	Recommended
CPU	4 cores	8+ cores
RAM	8 GB	16+ GB
Disk	20 GB free	100+ GB free (for datasets)
Network	Broadband internet	For downloading datasets and Docker images

Quick evaluation

For a quick evaluation with just the Eunomia demo dataset (~40 MB), the minimum specs are sufficient. The recommended specs are for loading the OMOP vocabulary (~16 GB) and genomic datasets.

Software Requirements

All Platforms

Software	Version	Purpose
Docker Desktop	24.0+	Container runtime
Docker Compose	v2+	Service orchestration (included with Docker Desktop)
Python	3.9+	Installer and dataset tools
Git	2.x	Cloning the repository

macOS

# Install Homebrew (if not already installed)
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install Docker Desktop
brew install --cask docker

# Install Python 3 and Git (usually pre-installed on macOS)
brew install python3 git

# Verify versions
docker --version        # Docker version 24.0+
docker compose version  # Docker Compose version v2+
python3 --version       # Python 3.9+
git --version           # git version 2.x

After installing Docker Desktop, launch it from Applications and wait for the Docker engine to start (whale icon in menu bar shows "Docker Desktop is running").

Apple Silicon (M1/M2/M3/M4)

Docker Desktop runs natively on Apple Silicon. All Parthenon containers are multi-arch (amd64 + arm64). No Rosetta translation needed.

Windows

1. Install WSL 2 (Windows Subsystem for Linux):

   # Run PowerShell as Administrator
   wsl --install

   Restart your computer when prompted.

2. Install Docker Desktop for Windows:

   • Download from docker.com/products/docker-desktop
   • During installation, ensure "Use WSL 2 instead of Hyper-V" is checked
   • Launch Docker Desktop and wait for it to start

3. Install Python 3 and Git:

   # Using winget (Windows Package Manager)
   winget install Python.Python.3.12
   winget install Git.Git

4. Open a WSL terminal for all subsequent commands:

   wsl

Windows users

All Parthenon commands should be run inside WSL 2 (Ubuntu), not PowerShell or CMD. Docker Desktop integrates with WSL 2 automatically.

Linux (Ubuntu/Debian)

# Install Docker Engine
curl -fsSL https://get.docker.com | sh

# Add your user to the docker group (avoids sudo for docker commands)
sudo usermod -aG docker $USER
newgrp docker

# Install Python 3 and Git
sudo apt update && sudo apt install -y python3 python3-pip git

# Verify
docker --version
docker compose version
python3 --version

Linux (RHEL/CentOS/Fedora)

# Install Docker Engine
sudo dnf install -y dnf-plugins-core
sudo dnf config-manager --add-repo https://download.docker.com/linux/fedora/docker-ce.repo
sudo dnf install -y docker-ce docker-ce-cli containerd.io docker-compose-plugin

# Start and enable Docker
sudo systemctl start docker
sudo systemctl enable docker
sudo usermod -aG docker $USER
newgrp docker

# Install Python 3 and Git
sudo dnf install -y python3 python3-pip git

Verify Your Environment

Run this quick check to confirm everything is ready:

# All platforms (run inside WSL on Windows)
docker --version && \
docker compose version && \
python3 --version && \
git --version && \
echo "" && \
echo "All prerequisites met!"

You should see version numbers for all four tools and the success message.

Optional: OMOP Vocabulary Download

If you plan to load the full OMOP vocabulary (recommended for production use), download it now while the installer runs:

1. Go to athena.ohdsi.org and create a free account
2. Click Download and select your vocabularies (at minimum: SNOMED, RxNorm, LOINC, ICD10CM)
3. Click Generate and wait for the download link email
4. Download the ZIP file (~4 GB) and note its path

The installer and dataset acquisition tool will ask for this file path during setup.

Next Step

Once prerequisites are met, proceed to Installing Parthenon.