The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

The Paper

Authors: Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter JA Cock, Björn Grüning, and Anton Nekrutenko

Journal: Genome Research, Volume 33(2):261–268

Published: February 2023

DOI: 10.1101/gr.276963.122

Research Overview

This paper presents Planemo as a comprehensive toolkit that addresses the complexity of integrating command-line software utilities into Galaxy’s web-based interface. It demonstrates how systematic tooling and best practices can accelerate scientific software development while maintaining quality.

Key Findings

Adoption & Impact: Planemo has achieved significant adoption with more than 70,000 downloads from both Anaconda and PyPI, demonstrating its value to the scientific software development community.

Multi-Domain Functionality: The toolkit encompasses:

• Galaxy tool development and testing
• Common Workflow Language (CWL) tool creation
• Workflow composition and execution
• Training material development for Galaxy

Technical Architecture

The paper details Planemo’s modular design using two central abstractions:

Runnables

Tools and workflows that can be executed across different computational environments.

Engines

External software capable of executing runnables (Galaxy, cwltool, Toil, etc.).

This abstraction layer enables developers to write tools once and execute them across multiple platforms.

Methodology & Best Practices

Planemo enforces development quality through:

• Test-driven development: Requires developers to write test cases before implementation
• Automated testing: Built-in test execution against multiple Galaxy versions
• Linting: Automated code quality checks and best practice enforcement
• Continuous integration: GitHub Actions and other CI workflows
• Dependency management: Automated updates for tool dependencies

Applications

The toolkit enables several advanced workflows:

1. Automated Dependency Updates: Keeps tools current with latest software versions
2. ToolShed Deployment: Manages tool releases to Galaxy’s public tool repository
3. Programmatic Workflow Execution: Enables high-throughput analyses via command-line interface
4. Training Material Integration: Facilitates creation of interactive tutorials

Personal Role & Contributions

As a co-author and core contributor to Planemo, my work focused on:

• Designing the “Runnables” and “Engines” abstraction layer
• Implementing Galaxy integration and testing frameworks
• Building deployment automation for the ToolShed
• Contributing to workflow execution capabilities
• Documentation and community engagement

The test-driven development approach was particularly important to me - by requiring test cases upfront, we created more robust tools and caught issues early in development.

Impact on Scientific Computing

Planemo has become essential infrastructure for the Galaxy ecosystem, enabling:

• Faster tool development cycles through automation
• Higher quality tools through enforced testing
• Broader accessibility by lowering the barrier to tool creation
• Reproducible research through standardized tool definitions
• Cross-platform compatibility via CWL support

Research Significance

This paper documents how systematic tooling can transform scientific software development. Rather than ad-hoc tool creation, Planemo provides a structured, tested, documented pathway from command-line utility to production-ready Galaxy tool.

The success of this approach - evidenced by 70,000+ downloads - demonstrates that the scientific community values tools that enforce best practices while reducing development friction.

Future Directions

The paper positions Planemo as a foundation for:

• Enhanced workflow composition interfaces
• Improved training material generation
• Broader CWL ecosystem integration
• Advanced testing and validation capabilities