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Installation

Requirements

  • Python 3.9 or later
  • pip package manager

Install from PyPI

The easiest way to install AnnoRefine is from PyPI:

pip install annorefine

This will install both the command-line tools and Python bindings.

Install from Source

To install from source (for development or latest features):

# Clone the repository
git clone https://github.com/nextgenusfs/annorefine.git
cd annorefine

# Install Rust (if not already installed)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Install maturin for building Python extensions
pip install maturin

# Build and install in development mode
maturin develop --release

# Or build a wheel
maturin build --release
pip install target/wheels/annorefine-*.whl

Verify Installation

Check that AnnoRefine is installed correctly:

# Check command-line tool
annorefine --version

# Check Python bindings
python -c "import annorefine; print(annorefine.version())"

Dependencies

AnnoRefine has minimal dependencies:

  • Rust dependencies (automatically handled during build):
  • rust-htslib for BAM file processing
  • rayon for parallel processing

  • clap for command-line interface

  • Python dependencies (automatically installed):

  • No additional Python dependencies required!

System Requirements

  • Memory: Depends on genome size and BAM file size. Typically 2-8 GB for most genomes.
  • Disk Space: Minimal, but ensure sufficient space for output files.
  • CPU: Multi-core recommended for parallel processing (use --threads option).

Platform Support

AnnoRefine is tested on:

  • Linux (Ubuntu 20.04+, CentOS 7+)
  • macOS (10.15+)
  • Windows (via WSL2)

Troubleshooting

Build Errors

If you encounter build errors when installing from source:

  1. Ensure Rust is up to date: 

    rustup update

  2. Ensure you have required system libraries: 

    # Ubuntu/Debian
sudo apt-get install build-essential libssl-dev pkg-config

# macOS
brew install openssl pkg-config

Import Errors

If you get import errors in Python:

  1. Ensure the package is installed: 

    pip list | grep annorefine

  2. Try reinstalling: 

    pip uninstall annorefine
pip install annorefine

Next Steps