Installation Guide

System Requirements

• Python 3.7+

• pip package manager

• 4GB RAM minimum (8GB+ recommended)

• 16GB+ RAM for biobank-scale data with GRM

Quick Installation

Install edge-gwas:

pip install git+https://github.com/nicenzhou/edge-gwas.git

Install external tools:

edge-gwas-install-tools

Verify installation:

edge-gwas-check-tools

Virtual Environment (Recommended)

# Create environment
python3 -m venv edge-gwas-env
source edge-gwas-env/bin/activate

# Install
pip install git+https://github.com/nicenzhou/edge-gwas.git
edge-gwas-install-tools

Optional Dependencies

File format support:

pip install pgenlib bgen-reader cyvcf2

Upgrading from v0.1.0

pip install --upgrade --force-reinstall git+https://github.com/nicenzhou/edge-gwas.git

Breaking changes:

• Koalas removed (now uses pandas)

• PCA functions return DataFrames with IID as index

• All sample IDs converted to strings

Troubleshooting

PLINK2/GCTA not found:

edge-gwas-install-tools
export PATH="$HOME/.local/bin:$PATH"

Memory errors with GRM:

from edge_gwas.utils import calculate_grm_gcta

grm_prefix = calculate_grm_gcta('genotypes', method='grm-sparse')

See Also

Documentation:

• Documentation Home - Home

• Installation Guide - Installation instructions and requirements

• Quick Start Guide - Getting started guide with simple examples

• Statistical Model - Statistical methods and mathematical background

• Example Workflows - Example analyses and case studies

• Visualization Guide - Plotting and visualization guide

• API Reference - Complete API documentation

• Troubleshooting Guide - Troubleshooting guide and common issues

• Frequently Asked Questions (FAQ) - Frequently asked questions

• Citation - How to cite EDGE in publications

• Changelog - Version history and release notes

• Advanced Topics for Further Updates - Planned features and roadmap

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Last updated: 2026-02-10 for edge-gwas v0.1.2

For questions or issues, visit: https://github.com/nicenzhou/edge-gwas/issues