install.sh

#!/usr/bin/env bash
# Installation script for WGS Extract v6 (Linux/macOS)

set -e  # Exit on error

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"

# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color

echo "=================================================="
echo "WGS Extract v6 - Installation"
echo "=================================================="
echo ""

# Detect platform
OS="$(uname -s)"
case "${OS}" in
    Linux*)     PLATFORM=Linux;;
    Darwin*)    PLATFORM=macOS;;
    *)          PLATFORM="UNKNOWN:${OS}"
esac

echo "Platform detected: ${PLATFORM}"
echo ""

# Check Python version
echo "Checking Python installation..."
if ! command -v python3 &> /dev/null; then
    echo -e "${RED}Error: Python 3 is not installed${NC}"
    echo "Please install Python 3.13 or later"
    exit 1
fi

PYTHON_VERSION=$(python3 --version | cut -d' ' -f2)
PYTHON_MAJOR=$(echo $PYTHON_VERSION | cut -d'.' -f1)
PYTHON_MINOR=$(echo $PYTHON_VERSION | cut -d'.' -f2)

echo "Python version: $PYTHON_VERSION"

if [ "$PYTHON_MAJOR" -lt 3 ] || ([ "$PYTHON_MAJOR" -eq 3 ] && [ "$PYTHON_MINOR" -lt 10 ]); then
    echo -e "${YELLOW}Warning: Python 3.13+ recommended, you have $PYTHON_VERSION${NC}"
    echo -e "${YELLOW}Some features may not work correctly${NC}"
fi

echo ""

# Check for samtools
echo "Checking for samtools..."
if command -v samtools &> /dev/null; then
    SAMTOOLS_VERSION=$(samtools --version | head -n1 | awk '{print $2}')
    echo -e "${GREEN}samtools found: version $SAMTOOLS_VERSION${NC}"
else
    echo -e "${YELLOW}Warning: samtools not found${NC}"
    echo "samtools is required for coverage calculations"
    echo "Install it using:"
    if [ "$PLATFORM" == "Linux" ]; then
        echo "  sudo apt-get install samtools   # Debian/Ubuntu"
        echo "  sudo yum install samtools       # RedHat/CentOS"
    elif [ "$PLATFORM" == "macOS" ]; then
        echo "  brew install samtools           # Homebrew"
        echo "  sudo port install samtools      # MacPorts"
    fi
fi

echo ""

# Check for BWA
echo "Checking for BWA..."
if command -v bwa &> /dev/null; then
    BWA_VERSION=$(bwa 2>&1 | grep Version | awk '{print $2}')
    echo -e "${GREEN}BWA found: version $BWA_VERSION${NC}"
else
    echo -e "${YELLOW}Warning: BWA not found${NC}"
    echo "BWA is required for alignment operations"
    echo "Install it using:"
    if [ "$PLATFORM" == "Linux" ]; then
        echo "  sudo apt-get install bwa        # Debian/Ubuntu"
        echo "  sudo yum install bwa            # RedHat/CentOS"
    elif [ "$PLATFORM" == "macOS" ]; then
        echo "  brew install bwa                # Homebrew"
        echo "  sudo port install bwa           # MacPorts"
    fi
fi

echo ""

# Create virtual environment
echo "Creating Python virtual environment..."
if [ -d "venv" ]; then
    echo -e "${YELLOW}Virtual environment already exists${NC}"
    read -p "Recreate it? (y/N): " -n 1 -r
    echo
    if [[ $REPLY =~ ^[Yy]$ ]]; then
        rm -rf venv
        python3 -m venv venv
    fi
else
    python3 -m venv venv
fi

echo ""

# Activate virtual environment
echo "Activating virtual environment..."
source venv/bin/activate

# Upgrade pip
echo "Upgrading pip..."
pip install --upgrade pip wheel setuptools

echo ""

# Install dependencies
echo "Installing dependencies..."
pip install -r requirements.txt

echo ""

# Install development dependencies (optional)
read -p "Install development dependencies? (y/N): " -n 1 -r
echo
if [[ $REPLY =~ ^[Yy]$ ]]; then
    pip install -r requirements-dev.txt
fi

echo ""

# Install package in editable mode
echo "Installing WGS Extract..."
pip install -e .

echo ""

# Create directories
echo "Creating directories..."
mkdir -p reference/genomes
mkdir -p reference/liftover
mkdir -p reference/microarray_templates
mkdir -p output
mkdir -p temp

echo ""

# Create launcher script
echo "Creating launcher script..."
cat > wgsextract.sh << 'EOF'
#!/usr/bin/env bash
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
source "$SCRIPT_DIR/venv/bin/activate"
python -m wgsextract "$@"
EOF
chmod +x wgsextract.sh

echo ""
echo -e "${GREEN}=================================================="
echo "Installation complete!"
echo "==================================================${NC}"
echo ""
echo "To run WGS Extract:"
echo "  1. Activate virtual environment:"
echo "     source venv/bin/activate"
echo "  2. Run the application:"
echo "     python -m wgsextract"
echo ""
echo "Or use the launcher:"
echo "     ./wgsextract.sh"
echo ""
echo "For help:"
echo "     python -m wgsextract --help"
echo ""