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.
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.
Quick Install
python -m venv .venv
.venv\Scripts\Activate.ps1
python -m pip install git+https://github.com/shivankvirdi/VepClin-MCP.git
Create a .env file in the folder where you will run VepClin
OPENROUTER_API_KEY=sk-or...
# Fill with your API key (see .env.example)
Install from Source
Follow .env.example & add API key to VepClin-MCP/.env (repo root)
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 .
Running VepClin-MCP
Run the terminal chat CLI:
vepclin
Run the MCP server directly:
python backend\mcp_server.py
