Installation¶

Quick install¶

pip install scvi-tools-mcp

or with uvx (no install needed, runs directly):

uvx scvi-tools-mcp

Add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{
  "mcpServers": {
    "scvi-tools": {
      "command": "uvx",
      "args": ["scvi-tools-mcp"]
    }
  }
}

claude mcp add scvi-tools-mcp uvx scvi-tools-mcp -s user

{ "command": "uvx", "args": ["scvi-tools-mcp"] }

The server itself does not require scvi-tools. Install it only if you want to run the knowledge refresh scripts locally:

pip install "scvi-tools-mcp[scvi]"

git clone https://github.com/Yoseflab/scvi-tools-mcp
cd scvi-tools-mcp
pip install -e ".[dev]"
pre-commit install
pytest