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ENCODE Toolkit MCP Server

local only

ENCODE Toolkit runs on your own machine — the client starts it, so there is no endpoint to ping. 342 installs a week from npm. Last commit 21 Sep 2026.

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

Installs per day peak 66 · avg 19 · -46% w/w
a month agotoday
342
Installs / week
pypi · encode-toolkit
20
Stars
0 open issues
21 Sep 2026
Last commit
0 releases in 90 days
AGPL-3.0
License
Python

What the code does

We read the source, 10 h ago · rules 3dff92dd89df

In the project's build, not in the package

Found in continuous integration, deployment or infrastructure files, or in a neighbouring package of the same monorepo. None of this is installed when you add the server: it describes how the project is built and released. We list it because a leaked key in a build pipeline is still a real problem, but it is not something this server does on your machine.

Builds a database query by concatenation .github/workflows/clone-count.yml:63
      - name: Update gist with accumulated data
        env:
          SECRET_TOKEN: ${{ secrets.SECRET_TOKEN }}

Is this your server and something here is wrong? Tell us — corrections are free and do not require a plan.

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.

Three servers free · no card

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.

run in your terminal
claude mcp add encode-toolkit -- uvx encode-toolkit
~/Library/Application Support/Claude/claude_desktop_config.json
{
  "mcpServers": {
    "encode-toolkit": {
      "args": [
        "encode-toolkit"
      ],
      "command": "uvx"
    }
  }
}
~/.codex/config.toml
[mcp_servers.encode-toolkit]
command = "uvx"
args = ["encode-toolkit"]
.cursor/mcp.json
{
  "mcpServers": {
    "encode-toolkit": {
      "args": [
        "encode-toolkit"
      ],
      "command": "uvx"
    }
  }
}
.vscode/mcp.json
{
  "mcpServers": {
    "encode-toolkit": {
      "args": [
        "encode-toolkit"
      ],
      "command": "uvx"
    }
  }
}

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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 pypi package encode-toolkit was installed 342 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 with the file path that client actually reads. It runs locally, so the command pulls encode-toolkit straight from pypi; nothing to host, nothing to sign up for.
How many people use ENCODE Toolkit?
The pypi package encode-toolkit was installed 342 times in the last week. Week over week that is -46%. 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.