install_packages

#!/bin/bash

pip install -r ./code/setup_pythonLibrary.txt

# Function to install MAFFT for Debian-based Linux
install_mafft_debian() {
    sudo apt-get update
    sudo apt-get install -y mafft
}

# Function to install MAFFT for Red Hat-based Linux
install_mafft_redhat() {
    sudo yum install -y mafft
}

# Function to install MAFFT for macOS
install_mafft_mac() {
    brew install mafft
    brew link --overwrite mafft 
}

# Detect the operating system
OS="$(uname -s)"

case "${OS}" in
    Linux*)     
        # Assuming a Debian-based or Red Hat-based Linux distribution
        if [ -f /etc/debian_version ]; then
            install_mafft_debian
        elif [ -f /etc/redhat-release ]; then
            install_mafft_redhat
        else
            echo "Unsupported Linux distribution"
        fi
        ;;
    Darwin*)    
        # macOS
        install_mafft_mac
        ;;
    *)          
        echo "Unsupported or unknown operating system: ${OS} - Predictions for new MHC allele sequences will not work."
        ;;
esac