# Recommended (any platform with Python)
pipx install genomemcp

# macOS (Homebrew)
brew install nexisdev/tap/genomemcp

# Windows (Scoop)
scoop bucket add genomemcp https://github.com/nexisdev/scoop-genomemcp
scoop install genomemcp

# From source
git clone https://github.com/nexisdev/GenomeMCP.git
cd GenomeMCP && ./install.sh

genomemcp search BRCA1              # 🔍 Search ClinVar
genomemcp variant 12345             # 📋 Get variant report
genomemcp gene TP53                 # 🧬 Get gene info
genomemcp pathway EGFR --visualize  # 🔬 Pathway analysis
genomemcp population 1-55516888-G-GA # 👥 gnomAD frequencies
genomemcp discover "Lynch Syndrome" # 🔗 Discover related genes
genomemcp tui                       # 🖥️ Interactive mode

genomemcp --theme cyberpunk search BRCA1
genomemcp --theme professional gene TP53
genomemcp --theme minimal pathway EGFR

# Clone the repository
git clone https://github.com/nexisdev/GenomeMCP.git
cd GenomeMCP

# Install dependencies with uv
uv sync

# Run the MCP server
uv run python src/main.py

# Using the install script
./install.sh

# Or with pip
pip install genomemcp[cli]

# Or for development
./setup-dev.sh
source .venv/bin/activate

{
  "mcpServers": {
    "genomemcp": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/GenomeMCP",
        "run",
        "python",
        "src/main.py"
      ]
    }
  }
}

### ☁️ Cloud Deployment (Railway)

You can deploy the GenomeMCP server to the cloud with one click. It will be exposed as an SSE (Server-Sent Events) endpoint, ready for remote agents.

1. Click the **Deploy on Railway** button above.
2. Provide your `SUPABASE_URL` and `SUPABASE_KEY` (optional, for persistence).
3. Connect your agent to the deployment URL (e.g. `https://your-app.up.railway.app/sse`).

---

## 📖 Usage Examples

### Search for a Gene Variant

### Get Population Frequency

### Discover Gene-Disease Relationships

### Visualize Pathways

```mermaid
graph TD
    TP53((TP53))
    TP53 --> P_123["Transcriptional Regulation by TP53"]
    TP53 --> P_456["Cell Cycle Checkpoints"]
    TP53 --> P_789["DNA Damage Response"]

GenomeMCP/
├── src/
│   ├── main.py          # MCP server & tool definitions
│   ├── clinvar.py       # ClinVar & PubMed API client
│   ├── genomics.py      # Exon/Intron mapping
│   ├── population.py    # gnomAD integration
│   ├── pathways.py      # Reactome integration
│   ├── utils.py         # Shared utilities
│   └── cli/             # Command-line interface
│       ├── app.py       # Typer CLI application
│       ├── formatters/  # Rich output formatters
│       ├── tui/         # Textual interactive UI
│       └── config.py    # Theme configuration
├── tests/               # Unit tests
├── docs/                # Documentation
├── install.sh           # Quick install script
├── setup-dev.sh         # Development setup
└── pyproject.toml       # Project configuration

# Run all tests
uv run pytest

# Run CLI tests
uv run pytest tests/test_cli.py -v

# Run specific test suite
uv run pytest tests/test_phase4.py tests/test_phase5.py