open-virome-mcp

OpenVirome MCP server

Getting Started

Install uv

It's recommended to use uv for package management and virtual env. It is required by the MCP python sdk to host the MCP inspection server which is useful for debugging.

See docs for installation: https://docs.astral.sh/uv/#installation

Set up virtual environment

uv venv
source .venv/bin/activate

Install dependencies

uv sync

Set up environment variables

Copy the example environment variables and fill in

cp .env.example .env

Run MCP inspector in browser

uv run mcp dev main.py

In left panel, enter command and argument values if not already pre-filled, then click 'Connect':

> Transport type: STDI
> Command: python
> Arguments: main.py

You may need to manually update 'Configuration' to increase timeout values if not setting them with server-config.json

> Request Timeout: 60000
> Maximum Total Timeout: 1200000

Run server locally

uv run main.py

Or with npx to use the config file:

npx @modelcontextprotocol/inspector --config server-config.json --server open-virome-mcp

Run MCP client integration

See server-config.json for additional config

{
  "mcpServers": {
    "open-virome-mcp": {
      "command": "python",
      "args": ["main.py"]
    }
  }
}

Notes

MCP reminders

• Resources are how you expose data to LLMs. They're similar to GET endpoints in a REST API - they provide data but shouldn't perform significant computation or have side effects.
• Tools let LLMs take actions through your server. Unlike resources, tools are expected to perform computation and have side effects. Tools will return structured results by default, if their return type annotation is compatible.
• Prompts are reusable templates that help LLMs interact with your server effectively:

Referenced repos:

• https://github.com/modelcontextprotocol/python-sdk

Formatting and linting

These can be added as github actions later

Format: black . or black --preview --enable-unstable-feature=string_processing .

Lint: pylint src