# Parabricks

Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness.

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: Writing
- License: CC-BY-4.0 AND Apache-2.0
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add NVIDIA/skills --skill parabricks -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill parabricks -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill parabricks -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill parabricks -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools, including planning-only questions.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Parabricks

## Purpose

Use this skill to discover the right NVIDIA Parabricks `pbrun` command, assess
runtime readiness, and generate version-aware command guidance for individual
tools.

Do **not** use this skill for whole-workflow inspection, acceleration planning,
or wiring optional GPU branches. For pipeline-level work, use
`genomics-workflow-acceleration`.

## When to Use This Skill

- Which `pbrun` tool fits the user's data and goal
- GPU, driver, Docker, container, storage, or installation readiness
- Command shape, flags, and validation for a specific Parabricks tool
- Reference/index compatibility and CPU-to-Parabricks option translation
- Troubleshooting a single Parabricks command or tool family
- Planning-only or "do not run" questions about a named `pbrun` tool (for
  example reference/index compatibility, output naming, or flag validity). Use
  this skill's references to answer; do not skip it because nothing will be
  executed.

## Prerequisites

- **Command guidance:** No Parabricks/NGC credential or local GPU/container
  runtime is required to read references or generate commands.
- **Readiness helper:** Requires Bash and GNU coreutils `timeout` (or `gtimeout`)
  on the host being inspected. Missing runtime components are reported as
  readiness gaps; without a timeout utility it exits before running probes.
- **STAR translation helper:** Requires Python 3.7 or newer, using only the
  standard library. It does not require a GPU or a Parabricks installation.
- **Execution:** The documented Docker commands require a supported Linux host,
  an NVIDIA GPU with sufficient memory, a compatible NVIDIA driver, Docker,
  NVIDIA Container Toolkit, and access to the selected Parabricks image.
  Pulling the image may require an NGC API key for authentication to [nvcr.io](https://nvcr.io).
  See [runtime-environment.md](references/runtime-environment.md) for
  version-specific requirements and checks.

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-parabricks/SKILL.md