bioinformatics-installer skillB
bioinformatics-installer is agent-read markdown (skill) from ammawla/encode-toolkit: 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 tools,.
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
# 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 environment is version-pinned for reproducibility and tested against ENCODE uniform processing standards. ## 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 callers, signal processors, statistical analysis frameworks in R, Python visualization and …
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How to install
mdr add ammawla/encode-toolkit/bioinformatics-installer@git:20260321.5cfbcfdmdr add ammawla/encode-toolkit/bioinformatics-installer@sha256:2150c3875b820ab9Pin 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_uhjlrm2rg3lcfxk6)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260321.5cfbcfd latest | 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
- fail: No curl or wget piped into a shell (matched: curl -s https://get.nextflow.io | bash)
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (31704 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
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_uhjlrm2rg3lcfxk6 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/bioinformatics-installer GET https://markdownregistry.com/api/v1/blob/2150c3875b820ab9f343972deeee9efced8ea0644df78d8c66719c5fc8eaf299
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