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ngs-runtime-env

Checks NGS tool availability and generates install plans before running sequencing pipelines.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#conda#ngs#install plan#Preflight#reference genome#sequencing pipeline
One-click install
npx skills add https://github.com/openai/plugins --skill ngs-runtime-env
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ngs-runtime-env
Source: https://github.com/openai/plugins/tree/main/plugins/ngs-analysis/skills/ngs-runtime-env
Command: npx skills add https://github.com/openai/plugins --skill ngs-runtime-env

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

NGS pipelines fail mid-run when required bioinformatics tools, references, or databases are missing. This Skill audits the local runtime environment first, so you know exactly what exists and what needs installing before launching a sequencing workflow.

Core Features & Use Cases

  • Existence Checks: Detects tools via PATH lookups, Python imports, and conda/mamba/micromamba/pip package listings before any download or install.
  • Install Planning: Emits reviewable install plans (install_plan.json plus a guarded install_commands.sh) that never install without explicit user approval.
  • Reference & Database Readiness: Plans, inventories, locks, and verifies reference genome and database bundles (e.g., GRCh38, Kraken2) separately from executable checks.
  • Use Case: Before running a shotgun metagenomics pipeline, generate a resource plan to confirm Kraken2 and optional Bracken/HUMAnN bundles are present, then hand off a reviewable setup checklist for anything missing.

Quick Start

Check which NGS tools already exist on this machine and emit an install plan for the missing ones without installing anything.

Frequently Asked Questions about ngs-runtime-env

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I check which NGS tools are installed before running a pipeline?▼

Run the preflight script with --list to audit executables on PATH, Python imports, and conda/mamba/pip packages. Add --pipeline with a workflow name like dna_variant_calling to check only the tools that pipeline requires.

How to generate an install plan for missing bioinformatics packages?▼

Use the preflight script with --emit-install-plan to produce a machine-readable install_plan.json and a guarded install_commands.sh. The shell script is review-only and will not install unless NGS_RUN_INSTALL_COMMANDS=1 is set after explicit approval.

Should I use conda, mamba, or containers for NGS tool installation?▼

For nf-core workflows, install Nextflow and use Docker, Singularity, or Apptainer profiles. For local execution, prefer mamba or micromamba environments from conda-forge and bioconda, and never modify the system Python.

How do I verify reference genomes and databases like Kraken2 are ready?▼

Use the reference manager's plan or check commands with --kind reference or database and a bundle name such as grch38_core or kraken2_standard. Missing required bundles block readiness, while optional bundles like Bracken or HUMAnN stay explicit.

Can the skill install tools automatically without my approval?▼

No. Installs only happen when you explicitly pass --install-missing --yes after reviewing the plan. By default the skill only checks existence and emits plans, keeping large downloads and environment changes deliberate.

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