setup SKILL.md skillB
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
setup from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/setup@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- B, 16 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
plugin/skills/setup/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 12,234 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# ENCODE Toolkit Setup
## When to Use
- User needs help installing or configuring the ENCODE Toolkit MCP server
- User is getting connection errors or server startup failures
- User asks "how do I set up ENCODE?" or "install ENCODE toolkit"
- User needs to configure ENCODE credentials for restricted data access
- User wants to verify their ENCODE server connection is working
- User is setting up a new environment and needs the ENCODE plugin
Help the user set up the ENCODE Toolkit server. The server connects Claude to the ENCODE Project genomics database — the largest public catalog of functional genomic elements with 8,000+ experiments across 50+ assay types.
## Installation
The ENCODE Toolkit server is installed via `uvx` (recommended) or `pip`:
### For Claude Code (CLI)
```bash
claude mcp add encode -- uvx encode-toolkit
```
### For Claude Desktop
Add to `claude_desktop_config.json`:
- **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
- **Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
```json
{
"mcpServers": {
"encode": {
"command": "uvx",
"args": ["encode-toolkit"]
}
}
}
```
Then restart Claude Desktop.
…Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/setup@sha256:1101898eace2afd0The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_dz6g5o6ter3lxkux)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 96 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 12,234 B | B | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 11,834 B | B | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 11,798 B | B | view |
Audit of the latest version
- fail: No curl or wget piped into a shell (matched: curl -LsSf https://astral.sh/uv/install.sh \| sh)
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12234 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Starting a new one? Use a template for SKILL.md on mdpantry, which passes every one of these checks and says what to change in it.
Source
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_dz6g5o6ter3lxkux GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/setup GET https://markdownregistry.com/api/v1/blob/1101898eace2afd06335b247f47db1565c14c52496bde112d8f5368cadf6531d
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
More from ammawla/encode-toolkit
Every file in ammawla/encode-toolkit