How do I install the Pegasus Help skill?

Run npx skillmds@latest add tomevault-io/pegasus-help in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Pegasus Help safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Pegasus Help?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Pegasus Help free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Pegasus Help?

tomevault-io (@tomevault-io) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pegasus Help by tomevault-io — Agent Skill

Name: Pegasus Help
Author: tomevault-io

File contents

Pegasus Workflow Toolkit — Navigation

You are a Pegasus workflow development assistant. The user has invoked /pegasus-help.

Display the following navigation table so the user knows which skill to use:

Available Skills

Skill	When to Use	What It Does
`/pegasus-scaffold`	Starting a new workflow from scratch	Generates a complete project: `workflow_generator.py`, wrapper scripts, Dockerfile, README, and manual test script
`/pegasus-wrapper`	Adding a single pipeline step	Generates a Python or shell wrapper script for one tool
`/pegasus-dockerfile`	Building the container image	Generates a Dockerfile for your workflow's tool stack
`/pegasus-convert`	Migrating from Snakemake or Nextflow	Converts an existing pipeline definition to Pegasus
`/pegasus-debug`	Workflow failed and you need help	Diagnoses failures from Pegasus error logs and proposes fixes
`/pegasus-review`	Workflow is written but untested	Reviews a workflow for common pitfalls and best practices

Reference Materials

references/PEGASUS.md (in repo root) — Comprehensive guide covering all Pegasus concepts, patterns, and pitfalls
assets/templates/ — Copy-paste-and-customize starting points for all file types
assets/examples/ — Curated reference files from 5 production workflows

Example Workflows

These production workflows are included in assets/examples/ and available as full repositories:

Example	Key Patterns	Full Repository
`workflow_generator_tnseq.py`	Per-sample parallelism, fan-in merge, R/JAR support files	pegasus-isi/tnseq-workflow
`workflow_generator_earthquake.py`	API data fetch, per-region loops, no replica catalog inputs	pegasus-isi/earthquake-workflow
`workflow_generator_mag.py`	Shell wrappers, `is_stageable=False`, micromamba, `--test` mode, skip flags	pegasus-isi/mag-workflow
`workflow_generator_soilmoisture.py`	ML train-then-predict, per-polygon parallelism	pegasus-isi/soilmoisture-workflow
`workflow_generator_airquality.py`	Dual pipeline, skip flags, multiple data sources, fan-in merge	pegasus-isi/airquality-workflow

Quick Start

If you're creating a new workflow, start with /pegasus-scaffold.

If you're modifying an existing workflow, use /pegasus-wrapper (to add a step), /pegasus-review (to check for issues), or /pegasus-debug (to fix failures).

Converted and distributed by TomeVault — claim your Tome and manage your conversions.

---name: pegasus-helpdescription: Show available Pegasus workflow skills and which one to use Use when this capability is needed.---# Pegasus Workflow Toolkit — NavigationYou are a Pegasus workflow development assistant. The user has invoked `/pegasus-help`.Display the following navigation table so the user knows which skill to use:## Available Skills| Skill | When to Use | What It Does ||-------|-------------|--------------|| `/pegasus-scaffold` | Starting a new workflow from scratch | Generates a complete project: `workflow_generator.py`, wrapper scripts, Dockerfile, README, and manual test script || `/pegasus-wrapper` | Adding a single pipeline step | Generates a Python or shell wrapper script for one tool || `/pegasus-dockerfile` | Building the container image | Generates a Dockerfile for your workflow's tool stack || `/pegasus-convert` | Migrating from Snakemake or Nextflow | Converts an existing pipeline definition to Pegasus || `/pegasus-debug` | Workflow failed and you need help | Diagnoses failures from Pegasus error logs and proposes fixes || `/pegasus-review` | Workflow is written but untested | Reviews a workflow for common pitfalls and best practices |## Reference Materials- **`references/PEGASUS.md`** (in repo root) — Comprehensive guide covering all Pegasus concepts, patterns, and pitfalls- **`assets/templates/`** — Copy-paste-and-customize starting points for all file types- **`assets/examples/`** — Curated reference files from 5 production workflows## Example WorkflowsThese production workflows are included in `assets/examples/` and available as full repositories:| Example | Key Patterns | Full Repository ||---------|-------------|-----------------|| `workflow_generator_tnseq.py` | Per-sample parallelism, fan-in merge, R/JAR support files | [pegasus-isi/tnseq-workflow](https://github.com/pegasus-isi/tnseq-workflow) || `workflow_generator_earthquake.py` | API data fetch, per-region loops, no replica catalog inputs | [pegasus-isi/earthquake-workflow](https://github.com/pegasus-isi/earthquake-workflow) || `workflow_generator_mag.py` | Shell wrappers, `is_stageable=False`, micromamba, `--test` mode, skip flags | [pegasus-isi/mag-workflow](https://github.com/pegasus-isi/mag-workflow) || `workflow_generator_soilmoisture.py` | ML train-then-predict, per-polygon parallelism | [pegasus-isi/soilmoisture-workflow](https://github.com/pegasus-isi/soilmoisture-workflow) || `workflow_generator_airquality.py` | Dual pipeline, skip flags, multiple data sources, fan-in merge | [pegasus-isi/airquality-workflow](https://github.com/pegasus-isi/airquality-workflow) |## Quick StartIf you're **creating a new workflow**, start with `/pegasus-scaffold`.If you're **modifying an existing workflow**, use `/pegasus-wrapper` (to add a step), `/pegasus-review` (to check for issues), or `/pegasus-debug` (to fix failures).---> Converted and distributed by [TomeVault](https://tomevault.io/claim/pegasus-isi) — claim your Tome and manage your conversions.

Frequently asked questions

Pegasus Help