Home / ammawla / encode-toolkit · GitHub

data-provenance SKILL.md skillA

This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.

data-provenance from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/data-provenance@git:20260920.6050003

Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: skills/data-provenance/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 8, 2026
Size: 26,652 bytes
Repository stars: 21
License: AGPL-3.0

Track exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and timestamps — to enable publication-ready methods writing. Use when the user processes ENCODE files, runs any bioinformatics tool, creates filtered/merged datasets, runs pipelines, performs liftover, uses R/Python/Bash for analysis, or needs to document their analysis chain for reproducibility and publication. Also use when the user says "write me methods" to auto-generate…

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

# Exact Provenance Tracking and Methods Writing

## When to Use

- User wants to track the full analysis chain from ENCODE download through processing to publication figure
- User asks about "provenance", "reproducibility", "methods section", or "analysis log"
- User needs to log derived files with their processing parameters for audit trail
- User wants to auto-generate publication-ready methods text from logged analysis steps
- Example queries: "log my peak calling step", "generate a methods section from my analysis", "show the provenance chain for this figure"

Track every operation on ENCODE data with exact tool versions, reference files, scripts, parameters, and timestamps to enable publication-ready methods sections.

## Scientific Rationale

**The question**: "What exactly was done to this data, and can someone else reproduce it identically?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/data-provenance@sha256:4d0e3d812cd15f47

The 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.

Badge

[![mdr](https://markdownregistry.com/badge/art_6ssxqiysztoaix7b.svg)](https://markdownregistry.com/a/art_6ssxqiysztoaix7b)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 3 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 98 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	26,652 B	A	view · diff
git:20260920.992a807	2026-09-20	992a807	25,112 B	A	view · diff
git:20260308.ca46af5	2026-03-08	ca46af5	25,103 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (26652 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 curl or wget piped into a shell
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

Source

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_6ssxqiysztoaix7b
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/data-provenance
GET https://markdownregistry.com/api/v1/blob/4d0e3d812cd15f4715194eb1462a76ba90bf567c9412852c132c8cc5cac38457

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.

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