Installation

Requirements

• Python 3.9 or higher

• pandas (https://pandas.pydata.org/)

• click (https://palletsprojects.com/p/click/)

• click-log (https://github.com/click-contrib/click-log)

Stable Release

To install the latest stable release, run:

$ pip install genotype_variants

This is the preferred method to install genotype_variants, as it will always install the most recent stable release.

For development or specific version installation:

$ pip install genotype_variants==0.3.10

Using pipx (Recommended for CLI tools)

For isolated installation of CLI applications, use pipx:

$ pipx install genotype_variants

From Source

For development or to get the latest features, you can install from source:

1. Clone the repository:

$ git clone https://github.com/msk-access/genotype_variants.git
$ cd genotype_variants

2. Install in development mode with all dependencies:

$ pip install -e '.[dev]'

This will install the package in editable mode along with development dependencies.

Docker

A Docker image is available for easy deployment:

$ docker pull ghcr.io/msk-access/genotype_variants:latest