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Installation

This page explains how to install the Genomic Knowledge Model (GKM) Toolkit and choose the optional dependencies you need.

Want to contribute to the GKM Toolkit?

This page describes installing the published GKM Toolkit package for using it. If you want to make code or documentation changes, use the editable source checkout and development dependencies described in Development and contributing.

Only want to read the notebooks?

No installation is needed. Go to Explore with notebooks to read the rendered walkthroughs online.

Prerequisites

You will need:

  • Python 3.11 or newer
  • Git
  • A terminal or command prompt

Set up a virtual environment

To use the example notebooks and data included in this repository, clone the repository, create a virtual environment, and activate it:

git clone https://github.com/ga4gh/gkm-starter-kit.git
cd gkm-starter-kit
python3 -m venv .venv
source .venv/bin/activate

Install the GKM Toolkit

With the virtual environment activated, install the published GKM Toolkit package from PyPI:

python3 -m pip install ga4gh.gkm --pre

Why do I need --pre?

This project uses pre-release versions of the GKM reference implementations.

Optional dependencies

Most users can start with the GKM Toolkit package alone. Add these extras only when you need the related capability:

  • notebooks — Run the example notebooks.
  • tests — Run the test suite.
  • dev — Change the GKM Toolkit's code and run code-quality checks.
  • docs — Build or edit the documentation.

You can install more than one at a time by separating them with commas. For example, this installs all optional dependencies:

python3 -m pip install "ga4gh.gkm[notebooks,tests,dev,docs]" --pre

Now that you're set up

Choose what you want to do next: