Install SAIGE-QTL using pixi

Prerequisites

• Linux or macOS (64-bit)
• Internet connection for downloading packages
• Sufficient disk space (~2-3 GB for all dependencies)
• No conda, mamba, or other package managers required
• Git (for downloading the source code)

Note: These steps can be found in the Dockerfile.

0. Download the SAIGE-QTL package from github

src_branch=main
repo_src_url=https://github.com/weizhou0/SAIGEQTL
git clone -b $src_branch $repo_src_url

1. Install pixi and the R packages

Option A: User-space Installation (No root required)

For Users Without Root Access (Recommended)

# Single command - installs in user directory
curl -fsSL https://pixi.sh/install.sh | sh && \
    export PATH="$HOME/.pixi/bin:$PATH" && \
    CONDA_OVERRIDE_GLIBC=2.28 pixi install --manifest-path=$PWD/SAIGEQTL/pixi.toml && \
    rm -rf ~/.cache/pixi && \
    CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=$PWD/SAIGEQTL/pixi.toml Rscript -e 'install.packages("lintools", repos="https://cloud.r-project.org")' && \
    CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=$PWD/SAIGEQTL/pixi.toml Rscript -e 'install.packages("remotes", repos="https://cloud.r-project.org"); remotes::install_github("barkasn/fastSave")'

Option B: System-wide Installation (Requires root - original approach)

For Root Users (System-wide Installation)

# Single command - Install pixi in user directory (recommended for most users)
curl -fsSL https://pixi.sh/install.sh | sh  && \
    export PATH="$HOME/.pixi/bin:$PATH" && \
    CONDA_OVERRIDE_GLIBC=2.28 pixi install --manifest-path=$PWD/SAIGEQTL/pixi.toml && \
    rm -rf ~/.cache/pixi  && \
    CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=$PWD/SAIGEQTL/pixi.toml Rscript -e 'install.packages("lintools", repos="https://cloud.r-project.org")'  && \
    CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=$PWD/SAIGEQTL/pixi.toml Rscript -e 'install.packages("remotes", repos="https://cloud.r-project.org"); remotes::install_github("barkasn/fastSave")' 

2. Install the SAIGE-QTL package

# Set the path to the SAIGEQTL/ source code

PATHTOSAIGEQTL=./

# Set the path to the file pixi.toml, which is in the SAIGEQTL folder 

PATHTOTOML=${PATHTOSAIGEQTL}SAIGEQTL/

Installation to the default R library paths

CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOTOML}pixi.toml R CMD INSTALL ${PATHTOSAIGEQTL}SAIGEQTL

When calling SAIGE-QTL in R, set the library location:

library(SAIGEQTL)

Alternative installation paths

For custom library installation to the specified R library location, e.g. path_to_final_SAIGEQTL_library

CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOTOML}pixi.toml R CMD INSTALL ${PATHTOSAIGEQTL}SAIGEQTL --library=path_to_final_SAIGEQTL_library

When calling SAIGE-QTL in R, set the library location:

library(SAIGEQTL, lib.loc=path_to_final_SAIGEQTL_library)

Change the library(SAIGEQTL) to library(SAIGEQTL, lib.loc=path_to_final_SAIGEQTL_library) in the wrapper files

${PATHTOSAIGEQTL}SAIGEQTL/extdata/step1_fitNULLGLMM_qtl.R
${PATHTOSAIGEQTL}SAIGEQTL/extdata/step2_tests_qtl.R
${PATHTOSAIGEQTL}SAIGEQTL/extdata/step3_gene_pvalue_qtl.R
${PATHTOSAIGEQTL}SAIGEQTL/extdata/makeGroupFile.R

What Gets Installed

SAIGE-QTL Source Code

• Repository: https://github.com/weizhou0/SAIGEQTL
• Branch: main (latest stable version)
• Local directory: SAIGEQTL/ (created by git clone)

Core Dependencies (from pixi.toml)

• Statistical Computing: R with numerical libraries (OpenBLAS, SuperLU)
• R Packages:
  • Statistical genetics: MetaSKAT, SKAT, SPAtest
  • Data manipulation: data.table, dplyr, dbplyr
  • Parallel computing: RcppParallel, furrr
  • Numerical computing: RcppArmadillo, RcppEigen, RcppNumerical
• System Libraries: boost-cpp, zlib, zstd, savvy

Additional R Packages

• lintools: Linear programming and optimization tools
• remotes: For installing packages from GitHub
• fastSave: Fast saving/loading of R objects (from GitHub)

Verification

After installation, verify the setup:

# Check if pixi environment is working
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOSAIGEQTL}SAIGEQTL/pixi.toml R --version

# Test SAIGE-QTL installation
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOSAIGEQTL}SAIGEQTL/pixi.toml Rscript -e 'library(SAIGEQTL); packageVersion("SAIGEQTL")'

#if not installed in the default folder for R libraries
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOSAIGEQTL}SAIGEQTL/pixi.toml Rscript -e 'library(SAIGEQTL, lib.loc=path_to_final_SAIGEQTL_library); packageVersion("SAIGEQTL")'

#For example
#CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOSAIGEQTL}SAIGEQTL/pixi.toml Rscript -e 'library(SAIGEQTL, lib.loc="/humgen/atgu1/fin/wzhou/projects/eQTL_method_dev/tool_dev/test_doc/install_test"); packageVersion("SAIGEQTL")'
##output: [1] '0.3.2.1'


# Check key dependencies
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOSAIGEQTL}SAIGEQTL/pixi.toml Rscript -e 'library(SKAT); library(MetaSKAT); library(data.table)'

---

✅ Next Steps

Installation Complete!

You’ve successfully installed SAIGE-QTL with Pixi. Here’s how to get started with your first analysis.

Your Command Prefix

All SAIGE-QTL commands will use this prefix:

CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOTOML}pixi.toml

💡 Tip: Set an alias to save typing:

# Add to your ~/.bashrc or ~/.bash_profile
alias saige-pixi='CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=/path/to/SAIGEQTL/pixi.toml'

# Then you can run:
saige-pixi Rscript 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

Example command for Pixi users:

# Step 1 example
CONDA_OVERRIDE_GLIBC=2.28 pixi run --manifest-path=${PATHTOTOML}pixi.toml \
    Rscript ${PATHTOSAIGEQTL}SAIGEQTL/extdata/step1_fitNULLGLMM_qtl.R \
    --phenoFile=phenotypes.txt \
    --phenoCol=ENSG00000123456 \
    --traitType=count \
    --outputPrefix=output/gene1

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:

1. Check the FAQ for common problems
2. Verify your installation using the verification commands above
3. Review the cis-eQTL tutorial for step-by-step guidance