Step 0 — Prerequisite
Before launching BiomiX 3.0, Docker must be installed on your system. The process differs slightly by platform — select yours below.
Requires Windows 10 (build 19045 or newer) or Windows 11, 64-bit, with at least 4 GB RAM. The installer handles all dependencies automatically.
Go to docker.com/products/docker-desktop and download the Windows installer (choose x64 or ARM64 based on your processor).
Double-click Docker Desktop Installer.exe and follow the setup wizard, keeping the default options selected.
The installer may ask you to restart your computer. Do so before continuing.
Open Docker Desktop from the Start menu and accept the terms of service. Once the whale icon in the system tray is stable, open PowerShell or CMD and run:
docker run hello-worldA welcome message from Docker confirms the installation is working.
If Docker does not start, see the troubleshooting section below.
Requires macOS 13 (Ventura) or later. Available for both Apple Silicon (M1/M2/M3/M4) and Intel. To check your chip: Apple menu → About This Mac.
Go to docker.com/products/docker-desktop and download the correct build for your chip: Apple Silicon or Intel.
Open the downloaded .dmg file and drag the Docker icon into your Applications folder.
Open Docker Desktop from Applications or Launchpad. Accept the terms of service and grant any permissions it requests. Docker will finish configuring itself automatically.
Once the whale icon in the menu bar is stable, open Terminal and run:
docker run hello-worldA welcome message from Docker confirms the installation is working.
On Linux, Docker Engine is installed directly from the command line — no desktop application needed, and no virtual machine required. Supported: Ubuntu 22.04, 24.04, 26.04 LTS (x86_64 or arm64). Instructions from the official Docker documentation.
Docker provides an official install script that handles everything automatically. Run the following two commands in your terminal:
curl -fsSL https://get.docker.com -o get-docker.sh
sudo sh get-docker.shAdd your user to the docker group so you do not need to type sudo before every Docker command. Log out and back in after running this:
sudo usermod -aG docker $USEROpen a new terminal session and run:
docker run hello-worldA welcome message from Docker confirms the installation is working.
| Platform | Component installed | Requires VM | Recommended for BiomiX |
|---|---|---|---|
| Windows | Docker Desktop | Yes (WSL 2, managed automatically) | Yes |
| macOS | Docker Desktop | Yes (Apple Virtualization Framework) | Yes |
| Linux (Ubuntu) | Docker Engine | No (native) | Yes, primary environment |
Common issues and how to fix them.
WSL 2 may not be installed or up to date. Open PowerShell as Administrator and run wsl --install or wsl --update, then restart your computer and try again.
Hardware virtualization may be disabled in your BIOS. To check: open Task Manager (Ctrl+Shift+Esc), go to the Performance tab, click CPU, and look for "Virtualization: Enabled". If it shows Disabled, you need to enable it in your BIOS/UEFI settings (usually under CPU or Advanced settings). The exact steps depend on your motherboard — search for your model + "enable virtualization BIOS".
The Docker service may not be running. Start it with sudo systemctl start docker and check its status with sudo systemctl status docker. To make it start automatically at boot: sudo systemctl enable docker.
You skipped the step adding your user to the docker group. Run sudo usermod -aG docker $USER, then log out and back in. Until then, prefix every Docker command with sudo.
Install Rosetta 2 for compatibility with tools built for Intel: open Terminal and run softwareupdate --install-rosetta.
Open an issue on the BiomiX issue tracker or contact us at cristian.iperi@univ-brest.fr.