Source Code Installation Guide (🔧 Advanced)

Overview

Source code installation is intended for developers, contributors, or users needing the latest development features.

We recommend the Pixi Source Installation method below, which handles all dependencies automatically. For other manual installation methods that require complex system configuration and troubleshooting, see Advanced Source Installation.

Pixi Source Installation (Recommended)

# Full environment management with pixi - cross-platform
# install pixi
curl -fsSL https://pixi.sh/install.sh | bash
# Restart shell or reload environment
export PATH="$HOME/.pixi/bin:$PATH"
# Download SAIGEQTL package from GitHub
git clone https://github.com/weizhou0/SAIGEQTL.git && cd SAIGEQTL
CONDA_OVERRIDE_GLIBC=2.28 pixi run install-standard

# Commands use manifest path:
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml Rscript extdata/step1_fitNULLGLMM_qtl.R --help

Why Pixi Source recommended?

✅ Managed environment: All dependencies handled automatically
✅ Cross-platform: Works on Linux and macOS
✅ Reproducible: Consistent across systems
✅ Development-ready: Full toolchain included
✅ No system configuration required: Unlike other source methods

Usage

Command Prefix

# Command prefix for all Pixi source installations
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=your_path_to_SAIGEQTL_folder/SAIGEQTL/pixi.toml

# Example commands:
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=your_path_to_SAIGEQTL_folder/SAIGEQTL/pixi.toml R -e 'library(SAIGEQTL); packageVersion("SAIGEQTL")'
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=your_path_to_SAIGEQTL_folder/SAIGEQTL/pixi.toml Rscript your_path_to_SAIGEQTL_folder/SAIGEQTL/extdata/step1_fitNULLGLMM_qtl.R --help

Command-Line Scripts

After installation, executable scripts are available:

cd your_path_to_SAIGEQTL_folder/SAIGEQTL
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml Rscript extdata/step1_fitNULLGLMM_qtl.R
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml Rscript extdata/step2_tests_qtl.R
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml Rscript extdata/step3_gene_pvalue_qtl.R

Custom Library Usage

Use the --library parameter with wrapper scripts:

cd your_path_to_SAIGEQTL_folder/SAIGEQTL
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml Rscript ./extdata/step1_fitNULLGLMM_qtl.R --library=/path/to/custom/library [other_options]

✅ Next Steps

Installation Complete!

You’ve successfully built SAIGEQTL from source using Pixi. Here’s how to get started with your first analysis.

Your Command Prefix

# Use pixi environment
cd your_path_to_SAIGEQTL_folder/SAIGEQTL
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml Rscript ./extdata/step1_fitNULLGLMM_qtl.R [options]

💡 Tip: Set up a convenient alias:

cd your_path_to_SAIGEQTL_folder/SAIGEQTL

# For Pixi source installation - add to ~/.bashrc or ~/.zshrc
alias saige-pixi='CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=pixi.toml'

# Then you can run:
saige-pixi Rscript extdata/step1_fitNULLGLMM_qtl.R --help

Quick Start Tutorial

Ready to run your first analysis? Follow this tutorial:

📖 cis-eQTL Analysis Tutorial - Learn how to map local genetic effects on gene expression

What you’ll learn:

How to prepare your data files
Running Step 1: Fit the null model
Running Step 2: Test genetic variants
Running Step 3: Calculate gene-level p-values

Additional Resources

Parameters & Options - Complete reference for all command-line parameters
Running Scripts Guide - Detailed information on running SAIGE-QTL scripts
FAQ - Common questions and troubleshooting

Need Help?

If you encounter issues:

Check the FAQ for common problems
Verify R can find the SAIGEQTL library
Review the cis-eQTL tutorial for step-by-step guidance

Advanced Source Code Installation