setup.sh

#!/bin/bash
# Linux/Mac Setup Script for Cancer@Home v2

echo "=================================="
echo "Cancer@Home v2 - Setup"
echo "=================================="
echo ""

# Check Python
echo "Checking Python installation..."
if command -v python3 &> /dev/null; then
    PYTHON_VERSION=$(python3 --version)
    echo "✓ Python found: $PYTHON_VERSION"
else
    echo "✗ Python not found. Please install Python 3.8+"
    exit 1
fi

# Check Docker
echo "Checking Docker installation..."
if command -v docker &> /dev/null; then
    DOCKER_VERSION=$(docker --version)
    echo "✓ Docker found: $DOCKER_VERSION"
else
    echo "✗ Docker not found. Please install Docker"
    exit 1
fi

# Create virtual environment
echo ""
echo "Creating Python virtual environment..."
python3 -m venv venv
echo "✓ Virtual environment created"

# Activate virtual environment and install dependencies
echo ""
echo "Installing Python dependencies..."
source venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
echo "✓ Dependencies installed"

# Create necessary directories
echo ""
echo "Creating directory structure..."
mkdir -p data/gdc
mkdir -p data/boinc
mkdir -p data/processed/fastq
mkdir -p data/processed/blast
mkdir -p data/processed/variants
mkdir -p data/cache
mkdir -p logs
echo "✓ Directories created"

# Start Docker containers
echo ""
echo "Starting Neo4j database..."
docker-compose up -d
sleep 10
echo "✓ Neo4j started"

echo ""
echo "=================================="
echo "Setup Complete!"
echo "=================================="
echo ""
echo "To start the application:"
echo "  1. Activate virtual environment: source venv/bin/activate"
echo "  2. Run the application: python run.py"
echo ""
echo "Access points:"
echo "  - Application: http://localhost:5000"
echo "  - Neo4j Browser: http://localhost:7474 (neo4j/cancer123)"
echo "  - API Docs: http://localhost:5000/docs"
echo ""