download-encode skillA
download-encode is agent-read markdown (skill) from ammawla/encode-toolkit: Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# Download ENCODE Files ## When to Use - User wants to download ENCODE data files to their local machine - User asks to "download", "get", or "fetch" ENCODE files - User needs specific file formats (BED, FASTQ, BAM, bigWig) from experiments - User wants to batch download files matching search criteria - User needs to verify file integrity after download (MD5 checksums) - User asks about organizing downloaded files by experiment or format Help the user download ENCODE data files to their local machine. ## Download Strategy 1. **Specific files by accession**: Use `encode_download_files` with file accession IDs (e.g., "ENCFF635JIA"). 2. **Batch download by criteria**: Use `encode_batch_download` to search and download in one step. - Always start with `dry_run=True` (default) to preview what will be downloaded - Show the user the file count, total size, and file list - Only proceed with `dry_run=False` after user confirms 3. **Download organization options**: - `"flat"`: All files in one directory - `"experiment"`: Organized by experiment accession (recommended) - `"format"`: Organized by file format …
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How to install
mdr add ammawla/encode-toolkit/download-encode@git:20260920.6050003mdr add ammawla/encode-toolkit/download-encode@sha256:739c6b24d1c151a0Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_drohmp57pyqwhayi)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 21,823 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 21,637 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 21,631 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (21823 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
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_drohmp57pyqwhayi GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/download-encode GET https://markdownregistry.com/api/v1/blob/739c6b24d1c151a0024642bbde843805962ddef3d5da01129944a42f9b896736
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