/bionemo-parabricks

name: parabricks
description: >-
  Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime
  readiness. Use for individual tools, including planning-only questions.
license: CC-BY-4.0 AND Apache-2.0
metadata:
  author: "Angel Pizarro <apizarro@nvidia.com>"
  version: "1.3.0"
  tags:
    - parabricks
    - genomics
    - nvidia

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](references/runtime-environment.md) for version-specific requirements and checks.

Tool scope: read this skill's references and user-supplied manifests; write only requested command artifacts. Use the bundled helpers for translation or an authorized host inspection. Documentation lookups use `docs.nvidia.com`; image access uses the selected registry only for authorized container execution. These instructions do not grant tool permissions; the host's permission policy still applies to shell, file, network and optional documentation MCP access.

Inputs

Use the user's explicit arguments and supplied manifests as the source of truth; use prior context only where it does not conflict. Read a named manifest before translating it. For command guidance, identify the assay, input paths, reference/index provenance, outputs and target release. Ask only for missing facts that change the answer; label unresolved template values as placeholders. Required inputs are the selected tool's read/reference and output arguments. Optional inputs include intervals, resource bundles, logs and tuning parameters when supported by that tool; do not invent them to fill a template. Runtime-only questions do not need sample metadata. Supplied deployment paths are not permission to probe local data or hardware.

If the user is unsure which tool applies, scan the **Tool Reference Index** below, then load the matching `references/pbrun-<tool>.md` file.

Limitations

This skill routes and guides Parabricks commands. It does not install Parabricks, infer missing sample metadata, guarantee output parity, provide clinical interpretation, or promise exact runtime without benchmark data.

Instructions

1. Identify the requested release. The option references cover v4.7.1; examples from another release are labeled. A software version and image tag can differ: NVIDIA's 4.7.1 image is tagged `4.7.1-1`. Preserve the user's verified image selection; use [command-conventions.md](references/command-conventions.md) for the shared launch and validation contract. 2. Classify the request:

• **Runtime** → [runtime-environment.md](references/runtime-environment.md)
• **Tool discovery** → **Tool Reference Index** (below)
• **Specific command** → matching `references/pbrun-<tool>.md`. Read it

**before** any web search or MCP lookup; use those only to verify version-sensitive details the reference does not settle. 3. Combine the tool-specific mapping with [shared-options.md](references/shared-options.md) rows whose **Tools** column names the selected command. For STAR argument arrays or multi-lane batches, use the local [translation helper](references/rna-translation.md); it preserves tokens and reports unmapped semantics without executing a workload. 4. Collect missing biological and filesystem context before generating commands. 5. Return the requested command or artifact with unresolved assumptions. For planning-only work, check command text against the references and supplied facts. Filesystem, container and output checks apply only to an authorized execution. Do not turn command preparation into a readiness inspection.

Available Scripts

Run these from the skill directory containing this file; paths are relative to that directory. See the helper prerequisites above.

| Script | Purpose | Arguments | | --- | --- | --- | | `scripts/check_parabricks_runtime.sh` | Inspect the execution host; report gaps without installing anything | `--path DIR` (repeatable), `--format text\|json`, `--timeout SECONDS`; container probes require `--run-container-check` or `--run-parabricks-check` with `--parabricks-version TAG` / `--parabricks-image IMAGE` | | `scripts/translate_star_to_parabricks.py` | Convert explicit STAR argument