Connect AI assistants to PhenoWorks projects, datasets, and analysis pipelines through MCP.
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# PhenoWorks MCP Connect your AI assistant to PhenoWorks with the Model Context Protocol (MCP). The assistant can find projects and datasets, inspect analysis modules, run pipelines, and retrieve results using your PhenoWorks account permissions. This package runs the MCP server that your assistant connects to. You need a running PhenoWorks server and an MCP-compatible assistant; installing this package does not install PhenoWorks or provide an AI model. ## Before you start - Use **Python 3.11 or newer**. - Have your PhenoWorks server URL, such as `https://your-phenoworks-server`. - Create an API key in your PhenoWorks account settings. Your server URL is the address of your own PhenoWorks installation, not the public documentation website. Both the server root and a URL ending in `/api` are accepted. ## Install Install from PyPI in a Python virtual environment: ```bash pip install phenoworks-mcp phenoworks-mcp --help ``` The PhenoWorks Python SDK and MCP runtime are installed automatically. To upgrade an existing installation, run `pip install --upgrade phenoworks-mcp`. If you already use [uv](https://docs.astral.sh/uv/), you can run the package without a separate install command: ```bash uvx phenoworks-mcp --help ``` ## Connect to Claude Desktop Follow the [Claude Desktop setup tutorial](docs/claude-desktop.md) to create a dedicated uv environment, configure your local PhenoWorks connection, and start chatting with Claude. ## Connect over local HTTP For a client that accepts a Streamable HTTP MCP URL, start the server in a terminal. For example, in a macOS or Linux shell: ```bash export PHENOWORKS_API_BASE_URL="https://your-phenoworks-server" export PHENOWORKS_PUBLIC_URL="https://your-phenoworks-app" export PHENOWORKS_API_KEY="YOUR_API_KEY" phenoworks-mcp ``` Leave the process running and add this **MCP server URL** to your assistant: ```text http://127.0.0.1:8787/mcp ``` There are three relevant URLs: `PHENOWORKS_API_BASE_URL` points to the Ph…
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