cucinellclark/bvbrc-data-mcp-server

BV-BRC Data MCP Server

A Model Context Protocol (MCP) server that provides access to BV-BRC (Bacterial and Viral Bioinformatics Resource Center) data through the bvbrc-solr-python-api module.

Features

• Access to genome and genome feature data
• Query capabilities for various BV-BRC data types
• Modular tool architecture for different data categories
• Flask-based MCP server implementation

Installation

Prerequisites

• Python >= 3.10
• pip

Install Required Dependencies

0. Create and activate a virtual environment:

python3 -m venv .venv
source .venv/bin/activate

First, install the bvbrc-python-api dependency:

1. Clone the bvbrc-python-api repository:

git clone https://github.com/cucinellclark/bvbrc-python-api.git
cd bvbrc-python-api

2. Install the bvbrc-python-api package:

pip install -U pip
pip install -e .

Install This MCP Server

After installing the bvbrc-python-api dependency, install the MCP server:

git clone https://github.com/cucinellclark/bvbrc-data-mcp-server.git
cd bvbrc-data-mcp-server
pip install -r requirements.txt

Configuration

The server uses a config.json file for configuration:

{
    "base_url": "https://www.bv-brc.org/api-bulk",
    "mcp_url": "127.0.0.1",
    "port": 8059,
    "default_limit": 1000,
    "auth_url": "https://user.patricbrc.org/authenticate"
}

Usage

Run the MCP server:

python http_server.py

The server will start on port 8059 (configurable in config.json).

OR set mcp server config file for Claude and Cursor:

{
  "mcpServers": {
    "bvbrc-data": {
      "command": "/path/to/python3",
      "args": ["/path/to/bvbrc-data-mcp-server/stdio_server.py"],
      "env": {
        "BVBRC_BASE_URL": "https://www.bv-brc.org/api-bulk",
        "BVBRC_DEFAULT_LIMIT": "1000"
      }
    }
  }
}

Health Check

The server provides a health check endpoint at /health that returns the server status.

Dependencies

• flaskmcp
• httpx >= 0.28
• bvbrc-solr-python-api

License

This project is part of the BV-BRC MCP Servers collection.