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. See runtime-environment.md for version-specific requirements and checks.