ENCODE Toolkit MCP Server

by ammawla Your server? Claim it

local only

ENCODE Toolkit runs on your own machine — the client starts it, so there is no endpoint to ping. 139 installs a week from pypi. Last commit 21 Sep 2026.

20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines

Installs per day peak 319 · avg 28 · -9% w/w

a month agotoday

139

Installs / week

npm · encode-toolkit

Stars

0 open issues

21 Sep 2026

Last commit

3 releases in 90 days

AGPL-3.0

License

Python

Nothing serious here today

Today is the operative word: we check ENCODE Toolkit every 15 minutes and re-read its code on every release. Watch it and you find out the day that stops being true.

Connect this server

This server runs on your own machine — install it with the package manager and the client starts it for you. Package name taken from the official registry entry.

Claude Code Claude Desktop Codex Cursor VS Code

run in your terminal

claude mcp add encode-toolkit -- npx -y encode-toolkit

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}

~/.codex/config.toml

[mcp_servers.encode-toolkit]
command = "npx"
args = ["-y", "encode-toolkit"]

.cursor/mcp.json

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}

.vscode/mcp.json

{
  "servers": {
    "encode-toolkit": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}

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ENCODE Toolkit — questions

Answers built from our own checks of this server.

Why is there no uptime for ENCODE Toolkit?

ENCODE Toolkit runs on your own machine over stdio — there is no network address to reach, so uptime cannot be measured for it by anyone. What can be measured is adoption: the npm package encode-toolkit was installed 139 times last week.

How do I connect ENCODE Toolkit?

Copy the ready config from this page. We generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each in the form that client actually reads. It runs locally, so the command pulls encode-toolkit straight from npm; nothing to host, nothing to sign up for.

How many people use ENCODE Toolkit?

The npm package encode-toolkit was installed 139 times in the last week. Week over week that is -9%. We show installs rather than GitHub stars on purpose: a star is a bookmark, an install is someone actually running it.

Is ENCODE Toolkit open source?

Yes — it is published under the AGPL-3.0 licence, written in Python and 20 stars on GitHub. The source link is on this page, so you can read exactly what it does with your data before you connect it.