# 1. Clone and setup
git clone https://github.com/Babajan-B/BioQC-MCP.git
cd fastqc-multiqc-mcp-server
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

# 2. Install prerequisites
brew install fastqc          # macOS
pip install multiqc

# 3. Test the server
./tests/test_mcp_server.sh

# 4. Configure in Claude/Cursor (see below)

# macOS
brew install fastqc
pip install multiqc

# Linux (Ubuntu/Debian)
sudo apt-get install fastqc
pip install multiqc

# Verify installation
fastqc --version
multiqc --version

# Clone repository
git clone https://github.com/Babajan-B/BioQC-MCP.git
cd fastqc-multiqc-mcp-server

# Create virtual environment
python3 -m venv venv
source venv/bin/activate  # Windows: venv\Scripts\activate

# Install Python dependencies
pip install -r requirements.txt

# Verify setup
./tests/test_mcp_server.sh

{
  "mcpServers": {
    "fastqc-multiqc": {
      "command": "/FULL/PATH/TO/venv/bin/python3",
      "args": ["/FULL/PATH/TO/fastqc-multiqc-mcp-server/src/server.py"]
    }
  }
}

# Copy example config
mkdir -p ~/Library/Application\ Support/Cursor/User/globalStorage
cp examples/cursor-mcp-config.json ~/Library/Application\ Support/Cursor/User/globalStorage/mcp.json

# Edit the file and update paths to your installation
# Then restart Cursor (⌘Q and reopen)

{
  "mcpServers": {
    "fastqc-multiqc": {
      "command": "/FULL/PATH/TO/venv/bin/python3",
      "args": ["/FULL/PATH/TO/fastqc-multiqc-mcp-server/src/server.py"],
      "env": {
        "PATH": "/usr/local/bin:/opt/homebrew/bin:${PATH}",
        "PYTHONUNBUFFERED": "1"
      }
    }
  }
}

# Run all checks
./tests/test_mcp_server.sh

# Test MCP protocol compliance
python3 tests/test_server_manually.py

# Launch Inspector for interactive testing
./tests/launch_inspector.sh

"Run FastQC analysis on sample1.fastq and sample2.fastq"
"Check the quality of all FASTQ files in ~/data/sequencing/"
"Create a MultiQC report for samples in ~/results/"

"Read the FastQC report at ~/results/sample_fastqc.html"
"What does the quality report say about adapter contamination?"
"Summarize the MultiQC report findings"

"Generate a line chart showing per-base quality scores"
"Create a bar chart comparing GC content across samples"
"Make a heatmap of quality metrics"

"Analyze all FASTQ files in ~/data/, generate FastQC reports, 
create a MultiQC summary, and show me a chart of overall quality scores"

# AI writes and executes this pipeline:
files = list_fastq_files('/Users/jaan/Desktop/Alaa')
print(f"Found {len(files)} FASTQ files")

# Process files
for f in files:
    result = run_fastqc([f['path']], output_dir='./qc_results')
    print(f"Analyzed: {f['name']}")

# Generate aggregate report
multiqc = run_multiqc('./qc_results', output_dir='./report')
print(f"MultiQC report: {multiqc['report']}")

# Return structured result
result = {
    "files_analyzed": len(files),
    "report_path": multiqc['report']
}

# Verify installation
which fastqc
which multiqc

# If not found, install
brew install fastqc  # macOS
pip install multiqc

# Check PATH in config
# Add to config JSON:
"env": {
  "PATH": "/usr/local/bin:/opt/homebrew/bin:${PATH}"
}

# Check dependencies
pip install -r requirements.txt

# Test server directly
source venv/bin/activate
python3 src/server.py
# Should show MCP protocol output

# Check syntax
python3 -m py_compile src/server.py

# Make scripts executable
chmod +x tests/*.sh
chmod +x src/server.py

fastqc-multiqc-mcp-server/
├── src/
│   ├── __init__.py
│   └── server.py              # Main MCP server
├── tests/                      # Testing utilities
│   ├── test_mcp_server.sh     # Automated verification
│   ├── test_server_manually.py# MCP protocol test
│   ├── test_real_fastqc.sh    # Real data test
│   └── launch_inspector.sh    # MCP Inspector launcher
├── examples/                   # Configuration examples
│   └── cursor-mcp-config.json
├── docs/                       # Additional documentation
│   ├── TESTING_WITH_INSPECTOR.md
│   ├── TESTING_COMPLETE.md
│   ├── DEPLOYMENT_CHECKLIST.md
│   └── COMPARISON_BIOINFOMCP.md
├── requirements.txt            # Python dependencies
├── CHANGELOG.md                # Version history
├── LICENSE                     # MIT License
└── README.md                   # This file

git clone https://github.com/Babajan-B/BioQC-MCP.git
cd fastqc-multiqc-mcp-server
./tests/test_mcp_server.sh  # Verify setup
# Then configure in Claude/Cursor