Conda/Bioconda Installation Guide (🥉 Cross-Platform)

Overview

Conda provides a cross-platform installation method for SAIGE-QTL with automatic dependency management. This method works well for users who already have conda environments or prefer traditional package managers.

Why Conda?

✅ Advantages:

• Automatic dependency management
• No compilation required
• Works on any system with conda (Linux/macOS/Windows)
• Cross-platform compatibility
• Isolated environment management
• Fast installation

⚠️ Requirements:

• Conda or Mamba package manager
• No R installation required (conda provides R)

Installation Options

Option 1: Direct Installation (Recommended)

# Install directly with conda
conda install -c aryarm r-saigeqtl

Option 2: Create New Environment

# Create new isolated environment with SAIGEQTL
conda create -n saigeqtl -c aryarm r-saigeqtl
conda activate saigeqtl

Option 3: Install Miniconda First (If needed)

# If you don't have conda, install miniconda first
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b
~/miniconda3/bin/conda install -c aryarm r-saigeqtl

Usage

Activate Environment (if using Option 2)

conda activate saigeqtl

Test Installation

# Use R with SAIGEQTL
R -e "library(SAIGEQTL); packageVersion('SAIGEQTL')"

# Use command-line tools
step1_fitNULLGLMM_qtl.R --help
step2_tests_qtl.R --help
step3_gene_pvalue_qtl.R --help

Platform-Specific Notes

Linux

• Full support with all features
• Pre-built packages available
• Fastest conda installation

macOS

• Good support for both Intel and Apple Silicon
• Automatic dependency resolution
• May require compilation for some dependencies

Windows

• Limited support - use WSL2 + conda for best results
• Docker recommended for native Windows

Troubleshooting

Common Issues

1. Channel Priority

   # Ensure correct channel priority
   conda config --add channels conda-forge
   conda config --add channels bioconda  
   conda config --add channels aryarm
   

2. Environment Conflicts

   # Create clean environment
   conda create -n saigeqtl-clean -c aryarm r-saigeqtl
   

3. Package Not Found

   # Update conda and try again
   conda update conda
   conda install -c aryarm r-saigeqtl