MCP Servers

VepClin-MCP

A terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.

README

VepClin-MCP

VepClin-MCP is a terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to look up variant consequences and clinical significance, presenting the results as clear, readable summaries in a Rich-powered CLI.

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The CLI uses a Gruvbox-styled Rich interface with persistent conversation history. Ask follow-up questions in the same session, use /clear to reset context, /help for input tips, and /exit to quit. </br>

Quick Install

Windows PowerShell

python -m venv .venv
.venv\Scripts\Activate.ps1
python -m pip install git+https://github.com/shivankvirdi/VepClin-MCP.git

macOS / Linux

python3 -m venv .venv
source .venv/bin/activate
python -m pip install git+https://github.com/shivankvirdi/VepClin-MCP.git

Create a `.env` file in the folder where you will run VepClin

Windows PowerShell:

Set-Content -Path .env -Value "OPENROUTER_API_KEY=sk-or..."

macOS / Linux:

printf "OPENROUTER_API_KEY=sk-or...\n" > .env

Fill with your OpenRouter API key. VepClin also checks OPENROUTER_API_KEY if it is already set as an environment variable.

Install from Source

Follow .env.example and add your API key to VepClin-MCP/.env in the repo root.

Windows PowerShell

git clone https://github.com/shivankvirdi/VepClin-MCP.git
cd VepClin-MCP
python -m venv .venv
.venv\Scripts\Activate.ps1
python -m pip install -e .
Copy-Item .env.example .env

macOS / Linux

git clone https://github.com/shivankvirdi/VepClin-MCP.git
cd VepClin-MCP
python3 -m venv .venv
source .venv/bin/activate
python -m pip install -e .
cp .env.example .env

Running VepClin-MCP

Run the terminal chat CLI:

vepclin

Running only MCP server

Most users don't need this. The vepclin chat CLI starts and uses the MCP tools automatically.

vepclin-server

If you installed from source, you can also run the server directly:

python backend/mcp_server.py

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