OakVar MCP Server

# OakVar MCP Server A [Model Context Protocol (MCP)](https://modelcontextprotocol.io/) server that exposes [OakVar](https://oakvar.readthedocs.io/)'s genomic variant analysis capabilities to AI assistants. **Supported MCP Clients:** Claude Desktop, ChatGPT Desktop, and other MCP-compatible clients. ## Quick Start ```bash # 1. Install OakVar and the MCP server pip install oakvar oakvar-mcp # 2. Setup OakVar (first time only) ov system setup # 3. Configure your MCP client (see SETUP.md) ``` 📖 **Full setup instructions**: See [SETUP.md](SETUP.md) ## What is This? This MCP server lets you control OakVar through AI assistants like Claude or ChatGPT. Instead of running command-line tools, you can simply ask: - *"What OakVar modules are installed?"* - *"Install the ClinVar annotator"* - *"Run OakVar on my VCF file with gnomAD annotation"* - *"Show me pathogenic variants from the results"* ## Features | Category | Capabilities | |----------|--------------| | **Pipeline** | Run annotations, generate reports (VCF, Excel, CSV) | | **Modules** | Install, update, list, search 200+ annotator modules | | **Data** | Query result databases, filter variants, export data | | **Development** | Create module templates, pack for distribution | ## Architecture ``` ┌─────────────────┐ MCP Protocol ┌──────────────────┐ │ Claude / │◄────────────────────►│ OakVar MCP │ │ ChatGPT │ (stdin/stdout) │ Server │ └─────────────────┘ └────────┬─────────┘ │ │ Python API ▼ ┌──────────────────┐ │ OakVar │ │ Variant Analysis │ └──────────────────┘ ``` ## Installation Note: OakVar and this MCP server must be installed in the same Python environment. If you use a virtual environment, configure your MCP client to use the full path to that environment's `oakvar-mcp` executable. <!-- ### From PyPI ```bash pip install oakvar-mcp ``` --> ### From Source ```bash git clone https://github.com/zaroganos/oakvar-mcp.git cd oakvar-mcp pip install -e . ``` ## Configuration ### Claude Desktop Add to `claude_desktop_config.json`: ```json { "mcpServers": { "oakvar": { "command": "oakvar-mcp" } } } ``` ### ChatGPT Desktop Add to `chatgpt_mcp_config.json`: ```json { "mcpServers": { "oakvar": { "command": "oakvar-mcp" } } } ``` 📖 **Config file locations and troubleshooting**: See [SETUP.md](SETUP.md) ## Available Tools (19) | Tool | Description | |------|-------------| | `oakvar_version` | Get OakVar version | | `oakvar_system_check` | Verify installation | | `oakvar_system_setup` | Configure OakVar | | `oakvar_modules_dir` | Get/set modules directory | | `oakvar_module_list` | List modules | | `oakvar_module_info` | Get module details | | `oakvar_module_install` | Install modules | | `oakvar_module_uninstall` | Remove modules | | `oakvar_module_update` | Update modules | | `oakvar_run` | Run annotation pipeline | | `oakvar_report` | Generate reports | | `oakvar_sqliteinfo` | Get database info | | `oakvar_filtersqlite` | Filter databases | | `oakvar_query` | Execute SQL queries | | `oakvar_new_module` | Create module templates | | `oakvar_new_exampleinput` | Create test inputs | | `oakvar_module_pack` | Pack for distribution | | `oakvar_store_fetch` | Refresh store cache | | `oakvar_store_register` | Register modules | ## Development ```bash # Clone and install in dev mode git clone https://github.com/zaroganos/oakvar-mcp.git cd oakvar-mcp pip install -e ".[dev]" # Run tests pytest tests/ -v ``` ## Project Structure ``` oakvar-mcp/ ├── oakvar_mcp/ │ ├── __init__.py │ ├── __main__.py │ └── server.py ├── tests/ │ └── test_server.py ├── pyproject.toml ├── README.md ├── SETUP.md ├── claude_desktop_config.example.json └── chatgpt_mcp_config.example.json ``` ## License MIT License ## Links - [OakVar Documentation](https://oakvar.readthedocs.io/) - [OakVar GitHub](https://github.com/zaroganos/oakvar) - [Model Context Protocol](https://modelcontextprotocol.io/)