setup.sh

#!/usr/bin/env bash

# WGS Extract v6 Setup Script
# Sets up virtual environment and installs all dependencies

set -e  # Exit on error

echo "╔═══════════════════════════════════════════════════════════════╗"
echo "║           WGS Extract v6 - Setup Script                      ║"
echo "╚═══════════════════════════════════════════════════════════════╝"
echo ""

# Check Python version
echo "1. Checking Python version..."
if ! command -v python3.13 &> /dev/null; then
    echo "❌ Error: python3.13 not found"
    echo "   Please install Python 3.13 or later"
    exit 1
fi

PYTHON_VERSION=$(python3.13 --version)
echo "   ✓ Found $PYTHON_VERSION"
echo ""

# Check external tools
echo "2. Checking external tools..."
MISSING_TOOLS=()

if ! command -v samtools &> /dev/null; then
    MISSING_TOOLS+=("samtools")
fi

if ! command -v bcftools &> /dev/null; then
    MISSING_TOOLS+=("bcftools")
fi

if ! command -v tabix &> /dev/null; then
    MISSING_TOOLS+=("tabix")
fi

if ! command -v java &> /dev/null; then
    MISSING_TOOLS+=("java")
fi

if [ ${#MISSING_TOOLS[@]} -gt 0 ]; then
    echo "   ⚠️  Warning: Missing tools: ${MISSING_TOOLS[*]}"
    echo "   Install with: sudo apt install samtools bcftools tabix default-jre"
    echo ""
    read -p "   Continue anyway? (y/n) " -n 1 -r
    echo
    if [[ ! $REPLY =~ ^[Yy]$ ]]; then
        exit 1
    fi
else
    echo "   ✓ All external tools found"
fi
echo ""

# Create virtual environment
echo "3. Creating virtual environment..."
if [ -d "venv" ]; then
    echo "   ⚠️  venv/ already exists"
    read -p "   Remove and recreate? (y/n) " -n 1 -r
    echo
    if [[ $REPLY =~ ^[Yy]$ ]]; then
        rm -rf venv
        python3.13 -m venv venv
        echo "   ✓ Virtual environment recreated"
    else
        echo "   ✓ Using existing virtual environment"
    fi
else
    python3.13 -m venv venv
    echo "   ✓ Virtual environment created"
fi
echo ""

# Activate virtual environment
echo "4. Activating virtual environment..."
source venv/bin/activate
echo "   ✓ Virtual environment activated"
echo ""

# Upgrade pip
echo "5. Upgrading pip..."
pip install --upgrade pip > /dev/null
echo "   ✓ pip upgraded"
echo ""

# Install requirements
echo "6. Installing WGS Extract dependencies..."
pip install -r requirements.txt
echo "   ✓ Dependencies installed"
echo ""

# Install Yleaf
echo "7. Installing bundled Yleaf..."
if [ -d "yleaf" ]; then
    pip install ./yleaf/
    echo "   ✓ Yleaf installed from ./yleaf/"
else
    echo "   ❌ Error: yleaf/ directory not found"
    exit 1
fi
echo ""

# Verify installation
echo "8. Verifying installation..."

# Check WGS Extract can be imported
if python3 -c "import wgsextract; print('WGS Extract:', wgsextract.__version__)" 2>/dev/null; then
    echo "   ✓ WGS Extract modules OK"
else
    echo "   ❌ WGS Extract import failed"
    exit 1
fi

# Check Yleaf
if python3 -c "import yleaf; print('Yleaf:', yleaf.__version__)" 2>/dev/null; then
    echo "   ✓ Yleaf OK"
else
    echo "   ❌ Yleaf import failed"
    exit 1
fi

# Check Yleaf command
if venv/bin/Yleaf -h &> /dev/null; then
    echo "   ✓ Yleaf command OK"
else
    echo "   ❌ Yleaf command failed"
    exit 1
fi

echo ""
echo "╔═══════════════════════════════════════════════════════════════╗"
echo "║                    Setup Complete!                            ║"
echo "╚═══════════════════════════════════════════════════════════════╝"
echo ""
echo "To run WGS Extract:"
echo "  ./wgsextract.sh"
echo ""
echo "First time users:"
echo "  1. Load a BAM/CRAM file from Settings tab"
echo "  2. Download reference genomes (Settings → Reference Library)"
echo "  3. Explore features in Extract Data and Analyze tabs"
echo ""