Installation Guide

This guide provides detailed instructions for installing modtector on different operating systems.

System Requirements

Minimum Requirements

Operating System: Linux, macOS, or Windows
Memory: 4 GB RAM (8 GB recommended for large datasets)
Storage: 2 GB free space
CPU: Multi-core processor recommended for parallel processing

Required Dependencies

Rust: Version 1.70 or higher
Cargo: Included with Rust installation

Installing Rust

Linux/macOS

Install Rust using rustup (recommended):

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
source ~/.cargo/env

Verify installation:

rustc --version
cargo --version

Windows

Download and run rustup installer:
- Visit https://rustup.rs/
- Download and run rustup-init.exe
- Follow the installation prompts
Verify installation:

rustc --version
cargo --version

Installing modtector

Method 1: Build from Source (Recommended)

Clone the repository:

git clone https://github.com/TongZhou2017/modtector.git
cd modtector

Build the project:

# Debug build (faster compilation)
cargo build

# Release build (optimized performance)
cargo build --release

Verify installation:

./target/release/modtector --version
./target/release/modtector --help

Method 2: Install via Cargo

Install directly from crates.io:

cargo install modtector

Alternatively, you can install a specific version:

cargo install modtector --version 0.15.4

Note: The latest version is available on crates.io.

Dependencies

modtector uses the following Rust crates:

[dependencies]
rust-htslib = "0.47.0"    # BAM file processing
bio = "2.0.1"             # Bioinformatics utilities
plotters = "0.3"          # Plotting and visualization
csv = "1.3"               # CSV file handling
rayon = "1.8"             # Parallel processing
clap = "4.5"              # Command-line argument parsing
chrono = "0.4"            # Date and time handling
rand = "0.8"              # Random number generation

These dependencies will be automatically downloaded and compiled during the build process.

Platform-Specific Notes

Linux

Ubuntu/Debian: May require additional packages:

sudo apt-get update
sudo apt-get install build-essential pkg-config libssl-dev

CentOS/RHEL: May require:

sudo yum groupinstall "Development Tools"
sudo yum install pkgconfig openssl-devel

macOS

Xcode Command Line Tools: Required for compilation:

xcode-select --install

Windows

Visual Studio Build Tools: Required for compilation
Git: Required for cloning the repository

Verification

After installation, verify that modtector is working correctly:

# Check version
modtector --version

# Check available commands
modtector --help

# Test with a simple command
modtector count --help

Troubleshooting

Common Issues

Rust not found:
- Ensure Rust is properly installed and in your PATH
- Run source ~/.cargo/env (Linux/macOS) or restart terminal
Build failures:
- Update Rust: rustup update
- Clean build: cargo clean && cargo build --release
Permission errors:
- Ensure you have write permissions in the installation directory
- Use sudo if necessary (not recommended for development)
Memory issues during compilation:
- Increase swap space or available RAM
- Use cargo build instead of cargo build --release for initial testing

Getting Help

If you encounter issues during installation:

Check the Troubleshooting Guide
Search existing issues on the GitHub repository
Create a new issue with detailed error information on GitHub

Next Steps

After successful installation:

Read the Quick Start Guide
Explore the User Guide
Try the Examples

Uninstallation

To remove modtector:

If installed via cargo:

cargo uninstall modtector

If built from source:

# Simply delete the cloned directory
rm -rf modtector

Remove Rust (optional):

rustup self uninstall