bioinformatics-installer 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.
bioinformatics-installer 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/bioinformatics-installer@git:20260920.6050003Pins 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
plugin/skills/bioinformatics-installer/SKILL.md- Versions recorded
- 7
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 36,699 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts, and Python requirements. Use when the user needs to set up a bioinformatics workstation, install tools for a specific assay, create reproducible environments, or troubleshoot dependency issues. Trigger on: install…
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
# Bioinformatics Installer for ENCODE Data Analysis Install all bioinformatics tools needed for ENCODE data analysis, organized by assay type. This skill provides ready-to-use conda environment definitions, R/Bioconductor install scripts, Python package lists, and Nextflow pipeline infrastructure setup. Every primary tool is version-pinned for reproducibility; a few utility packages (`bedops`, `ucsc-bedgraphtobigwig`, `pigz`, `openjdk`, `r-base`) float so the solver can satisfy the pinned tools around them. ## When to Use - User wants to install bioinformatics tools needed for ENCODE data analysis - User asks about "install tools", "conda environment", "setup bioinformatics", or "install HOMER/MACS2/deeptools" - User needs pre-configured conda environments for specific assay pipelines (ChIP-seq, ATAC-seq, RNA-seq, etc.) - User wants to install R/Bioconductor packages (DESeq2, Seurat, ChIPseeker) or Python packages (Scanpy, pysam) - Example queries: "install tools for ChIP-seq analysis", "set up a conda environment for ATAC-seq", "install deeptools and bedtools" ## Overview ENCODE data analysis requires a broad ecosystem of tools spanning command-line aligners, peak …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/bioinformatics-installer@sha256:676b7cc5d5d1f79bThe 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_uhjlrm2rg3lcfxk6)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 7 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 32 days. Its first recorded version is graded B and its latest A.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 36,699 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 35,954 B | A | view · diff |
| git:20260920.bc6cada | 2026-09-20 | bc6cada | 32,168 B | A | view · diff |
| git:20260920.e0e9332 | 2026-09-20 | e0e9332 | 31,989 B | A | view · diff |
| git:20260920.67aff7f | 2026-09-20 | 67aff7f | 31,802 B | B | view · diff |
| git:20260321.5cfbcfd | 2026-03-21 | 5cfbcfd | 31,704 B | B | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 31,639 B | B | 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 (36699 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 · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_uhjlrm2rg3lcfxk6 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/bioinformatics-installer GET https://markdownregistry.com/api/v1/blob/676b7cc5d5d1f79b4c01987f7f806a0c478eb573079ebb08ac55af9983b2881a
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