Installation

Requirements

To install gentropy one needs to have pre installed:

• Python >=3.10, <3.13
• PySpark >=3.5.0, <3.6
• Java 11, 17 (for hail support Java 11 is recommended, see troubleshooting for more details)

Installation

To install Gentropy we recommend using uv, which is a tool for managing Python environments and dependencies.

uv add gentropy

Pypi

We recommend installing Open Targets Gentropy using Pypi:

pip install gentropy

Source

Alternatively, you can install Open Targets Gentropy from source. Check the contributing section for more information.

For any issues with the installation, check the troubleshooting section.

xgboost

To use gentropy LocusToGene model the xgboost package is required. To reduce the size of the dependencies, gentropy uses the full xgboost package only when xgboost-cpu is not available:

• amd64 and x86_64 will utilize xgboost-cpu.
• arm64 and aarch64 will utilize xgboost.

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• 2022-10-01
• 2025-09-03
• Contributors
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