Installing SAIGE-QTL

Choose the installation method that best fits your environment and requirements. We recommend Pixi for most users as it provides the most reliable and reproducible installation experience.

Current Version: 0.3.2

Updated: July 28, 2025

Installation Methods

🚀 Recommended: Pixi Installation

The fastest and most reliable method with automatic dependency management.

→ Install with Pixi

🐳 Docker Installation

Pre-built container for immediate use without local installation.

→ Install with Docker

📦 Conda/Bioconda Installation

Traditional package manager for Python/R environments.

→ Install with Conda

🔧 Source Code Installation

For advanced users who need custom builds or development versions.

→ Install from Source

Quick Start Comparison

Method Best For Setup Time Dependencies
Pixi Most users, reproducible environments ~5 minutes Automatic
Docker Containers, HPC clusters ~2 minutes Docker only
Conda Existing conda environments ~10 minutes Manual
Source Developers, custom builds ~30 minutes Manual

System Requirements

Minimum Requirements

  • OS: Linux, macOS, or Windows (WSL recommended)
  • RAM: 8GB minimum, 16GB+ recommended for large datasets
  • Storage: 2GB for software, additional space for data
  • R: Version 4.0+ (installed automatically with Pixi/Docker)
  • RAM: 32GB+ for large-scale analyses
  • CPU: Multi-core processor for parallel processing
  • Storage: SSD storage for improved I/O performance

What’s New in Version 0.3.2

✨ New Features

  • --offsetCol parameter: Use log of total read counts per cell as an offset in the model
  • Enhanced Pixi support: Improved installation process and environment management
  • Better error handling: More informative error messages and debugging information

🐛 Bug Fixes

  • Resolved memory issues with large datasets
  • Fixed compatibility issues with newer R versions
  • Improved handling of edge cases in variance estimation

📋 Complete Changelog

For detailed logs of all bug fixes and improvements, see the Installation Logs.

Post-Installation

Verify Installation

After installation, verify SAIGE-QTL is working correctly:

  1. Check help information: 
    # Replace with your installation method's command prefix
Rscript step1_fitNULLGLMM_qtl.R --help
  2. Run example analysis: Follow the Step 1 tutorial with provided example data

Next Steps

  1. Review the workflow overview - Understand the analysis pipeline
  2. Learn how to call SAIGE-QTL - Execute scripts in different environments
  3. Start with Step 1 - Begin your first analysis

Getting Help

Installation Issues

  • Check the specific installation guide for your chosen method
  • Verify system requirements are met
  • Review error messages carefully - they often contain helpful information

Technical Support

  • Email: wzhou@broadinstitute.org
  • GitHub Issues: For bug reports and feature requests
  • Documentation: Browse all available guides in the navigation menu

Changelog

**July 31, 2025:

  • Export extdata/ in the docker container so users do not need to download the git repo when using the docker image wzhou88/saigeqtl:latest on example data

Version 0.3.2 (July 28, 2025)

  • New: Added --offsetCol option for using log of total read counts per cell as an offset in the model
  • Improved: Enhanced installation process using pixi
  • Fixed: Various bug fixes and stability improvements