How do I install Snakemake?

Copy the stdio config for Cursor, Claude Desktop, Claude Code, or VS Code on this page. It uses the publisher's install, not a PlugMCP proxy.

Does Snakemake need an API key?

No required environment variable is listed on this record.

What transport does Snakemake use?

Snakemake runs locally over stdio.

When was Snakemake last checked?

Last checked 2026-11-10. Snakemake MCP: 20 real tools to read, check, lint, scaffold, build and run Snakemake code.

Snakemake MCP server

Power your agent

Add this server

The publisher's own command. Not a PlugMCP endpoint.

Add to Cursor Add to VS Code Run on PlugMCP

Host a copy with our keys and logs.

Local command

npx -y @mrfentmen/[email protected]

Claude Code has no install link for a local command. Copy the command below and run it in a terminal.

shClaude Code

1claude mcp add io.github.mrfentmen-snakemake-mcp -- npx -y @mrfentmen/snakemake-mcp@1.0.0

Run in a terminal.

jsonClaude Desktop

1{2  "mcpServers": {3    "io.github.mrfentmen-snakemake-mcp": {4      "command": "npx",5      "args": [6        "-y",7        "@mrfentmen/[email protected]"8      ]9    }10  }11}

claude_desktop_config.json

Local · npmPublisher installStep-by-step: add this in Claude

Remote URL or a command on your machine? How the two installs differ

Run on PlugMCP

Host a copy with our keys and logs.

A new server you create. It is not this listing's official endpoint. Use the publisher install when you want their URL and their credentials.

Launch

Server facts

Local

Transport: stdio
Version: 1.0.0
Last checked

Tools

No tool list yet. Remote servers get one after the first health check.

FAQ

Snakemake

Add this server

Host a copy with our keys and logs.

Server facts

Tools

Questions

How do I install Snakemake?

Does Snakemake need an API key?

What transport does Snakemake use?

When was Snakemake last checked?

Documentation