Docker setup
If you prefer working with Docker or you don’t want to install G4X-helpers locally, you can run its CLI tools from the Docker image that is published along with the repository.
If you have Docker already installed (or Apptainer, Podman ... ) and are familiar with using it, you can continue to the G4X-helpers Docker usage section.
Otherwise, please read on to get started.
Why use Docker?
- no local installs: skip creating a Python environment.
- reproducibility: everyone uses the same environment.
- isolated: nothing leaks into (or depends on) your system Python.
- great for HPC/servers: just bind your data directories.
1. install Docker
Docker is available for most platforms. Please refer to the Docker installation guide for Docker Engine (Linux), or Docker Desktop (MacOS/Windows). If you are not sure if Docker is already installed, you can simply call docker --version in your terminal.
2. pull the G4X-helpers image
The docker pull command downloads the G4X-helpers container image (and all of its layers) from GitHub’s Container Registry ( ghcr.io ) to your local Docker cache.
Once the image is pulled, you can start new containers from it instantly — even when you’re offline — without re-fetching data from the registry.
Tip
latest will always retrieve the most recently published build.
You can replace it with an explicit tag, which locks you to a reproducible version.
e.g. ghcr.io/singular-genomics/g4x-helpers:v0.4.11
if the pull was successful, you can confirm that the image is available by calling
You are now ready to use the G4X-helpers Docker image.
Please refer to the Docker usage section to learn how to run the tools.
3. updating & cleanup
You can update your image by running docker pull again
Over time, old images, stopped containers and dangling volumes can consume disk space.
A useful one-shot cleanup command is:
⸻