OakVar MCP Server
A Model Context Protocol (MCP) server that exposes OakVar's genomic variant analysis capabilities to AI assistants.
Supported MCP Clients: Claude Desktop, ChatGPT Desktop, and other MCP-compatible clients.
Quick Start
# 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
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 Source
git clone https://github.com/zaroganos/oakvar-mcp.git
cd oakvar-mcp
pip install -e .
Configuration
Claude Desktop
Add to claude_desktop_config.json:
{
"mcpServers": {
"oakvar": {
"command": "oakvar-mcp"
}
}
}
ChatGPT Desktop
Add to chatgpt_mcp_config.json:
{
"mcpServers": {
"oakvar": {
"command": "oakvar-mcp"
}
}
}
📖 Config file locations and troubleshooting: See 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
# 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