MCP Server¶

ClawBio ships a Model Context Protocol server, so any MCP-capable client can discover, read, and run bioinformatics skills. It runs locally over stdio. Your data never leaves your machine.

Claude Code users

Prefer the plugin, which installs the skills themselves rather than a remote-call shim: /plugin marketplace add ClawBio/ClawBio then /plugin install clawbio.

Quick start¶

No installation required. uvx fetches and runs it in a throwaway environment:

uvx --from 'clawbio[mcp]' clawbio mcp

If you prefer a permanent install:

pip install 'clawbio[mcp]'
clawbio mcp

Client configuration¶

The same three lines work across clients; only the file location differs.

CursorClaude DesktopVS CodeZed

~/.cursor/mcp.json (global) or .cursor/mcp.json (per project):

{
  "mcpServers": {
    "clawbio": {
      "command": "uvx",
      "args": ["--from", "clawbio[mcp]", "clawbio", "mcp"]
    }
  }
}

~/Library/Application Support/Claude/claude_desktop_config.json on macOS, %APPDATA%\Claude\claude_desktop_config.json on Windows:

{
  "mcpServers": {
    "clawbio": {
      "command": "uvx",
      "args": ["--from", "clawbio[mcp]", "clawbio", "mcp"]
    }
  }
}

.vscode/mcp.json in your workspace:

{
  "servers": {
    "clawbio": {
      "type": "stdio",
      "command": "uvx",
      "args": ["--from", "clawbio[mcp]", "clawbio", "mcp"]
    }
  }
}

settings.json:

{
  "context_servers": {
    "clawbio": {
      "command": {
        "path": "uvx",
        "args": ["--from", "clawbio[mcp]", "clawbio", "mcp"]
      }
    }
  }
}

Restart the client, then ask it something like "list the ClawBio pharmacogenomics skills and run the pharmgx demo".

Tools¶

Tool	Purpose
`clawbio_list_skills(query)`	Search the skill catalog. An empty query returns everything. Each result carries a `runnable` flag.
`clawbio_describe_skill(name)`	Return a skill's full `SKILL.md` contract: inputs, outputs, safety rules, demo command. Accepts either the skill name or its CLI alias.
`clawbio_run_skill(skill, demo, input_path, output_dir, extra_args)`	Execute a skill and return its structured result, including output file paths.

Not every skill is executable¶

The catalog contains both executable skills and agent-readable ones that ship only a SKILL.md contract. clawbio_list_skills marks each with a runnable boolean, and clawbio_run_skill refuses non-runnable skills with an explicit message rather than failing obscurely. Agents should not have to guess.

Data safety¶

By default the server runs demo data only. Passing input_path or output_dir is refused:

This ClawBio MCP server is restricted to demo data. To let it read and write
local files, restart it with CLAWBIO_MCP_ALLOW_LOCAL_FILES=1.

This is deliberate. Adding an MCP server to a client config is a low-friction action, often done once and forgotten, and it should not silently grant an agent read access to a patient genome. To analyse your own files, opt in explicitly:

{
  "mcpServers": {
    "clawbio": {
      "command": "uvx",
      "args": ["--from", "clawbio[mcp]", "clawbio", "mcp"],
      "env": { "CLAWBIO_MCP_ALLOW_LOCAL_FILES": "1" }
    }
  }
}

Skill runs still write a reproducibility/ bundle (commands.sh, environment.yml, SHA-256 checksums) next to their output, so an agent-initiated analysis can be replayed and checked without the original session.

There is no hosted ClawBio MCP endpoint, and this is a design decision rather than a gap. Genomic data should not traverse a third-party server to be analysed.

Requirements¶

Python 3.11+
mcp>=1.9,<2 — installed automatically by the [mcp] extra

mcp 2.0

mcp 2.0 removed mcp.server.fastmcp. The clawbio[mcp] extra pins below 2.0. If you installed mcp yourself and see a startup error naming the version, install the extra instead of a bare mcp.

Troubleshooting¶

Client shows no tools. Confirm the server starts on its own first:

uvx --from 'clawbio[mcp]' clawbio mcp

It should wait silently for input on stdin. Press Ctrl-C to exit. If it exits immediately with a message, the message names the cause.

uvx: command not found. Install uv, or use the pip install 'clawbio[mcp]' route and set "command": "clawbio", "args": ["mcp"].

A skill fails with a missing dependency. Some skills declare extra requirements. Run clawbio_describe_skill and check the dependencies field.