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pegasus-dockerfile

Generates Dockerfiles for Pegasus workflow container images with pip or micromamba.

Updated Feb 11, 2026
Search Tags:#workflow automation#pip#dependency management#containerization#dockerfile#pegasus wms#micromamba
One-click install
npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-dockerfile
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pegasus-dockerfile
Source: https://github.com/pegasus-isi/pegasus-workflow-toolkit/tree/main/.claude/skills/pegasus-dockerfile
Command: npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-dockerfile

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the creation of Dockerfiles, ensuring that all necessary tools and dependencies for a Pegasus workflow are correctly packaged into a container image.

Core Features & Use Cases

  • Dockerfile Generation: Creates Dockerfiles tailored to specific workflow requirements, supporting both pip and micromamba package managers.
  • Dependency Management: Helps identify and include all required system and Python packages, handling potential version conflicts.
  • Use Case: You need to deploy a complex bioinformatics workflow on Pegasus. This Skill will help you generate a Dockerfile that includes all the specialized bioinformatics tools and Python libraries, ensuring your workflow runs consistently in a containerized environment.

Quick Start

Use the pegasus-dockerfile skill to generate a Dockerfile for a workflow that requires Python 3.8, pandas, and samtools.

Frequently Asked Questions about pegasus-dockerfile

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

FAQPage Schema
How do I create a Dockerfile for a Pegasus workflow with Python and system dependencies?▼

To create a Dockerfile for a Pegasus workflow, you generate one that consolidates Python libraries and system dependencies into a single container image, using either pip or micromamba package managers.

What is the best way to package bioinformatics tools for Pegasus workflow containerization?▼

Packaging bioinformatics tools for Pegasus containerization involves generating a Dockerfile that includes all specialized tools, Python libraries, and headless support to ensure consistent workflow execution in a containerized environment.

Does Pegasus workflow containerization support both micromamba and pip dependency management?▼

Yes, Pegasus workflow containerization supports both micromamba and pip dependency management, allowing you to specify required Python libraries and handle potential version conflicts within the generated Dockerfile.

Can I embed wrapper scripts directly inside a Pegasus workflow Dockerfile?▼

Yes, you can embed wrapper scripts directly inside a Pegasus workflow Dockerfile, which ensures robust deployment and consistent execution of your workflow tools within the generated container image.

Why do I need a single container image for Pegasus workflow automation?▼

You need a single container image for Pegasus workflow automation to ensure reproducible execution environments by consolidating all workflow tools, system dependencies, and Python libraries together, eliminating environment discrepancies.

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