Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability

Join us for an intensive, week-long, in-person training designed to elevate your Galaxy expertise to new heights. This workshop is tailored for data scientists, advanced Galaxy users, and team leaders who need to scale, automate, and publish their data analysis workflows for batch processing and production-level applications.

Over five days, you’ll embark on a comprehensive journey through Galaxy’s advanced capabilities:

• Monday: Introduction & Workflow Development

  Start with a welcome and icebreaker to foster collaboration, followed by a brief overview of Galaxy and its workflow features. Dive into hands-on workflow development, where you’ll learn to design clean, efficient workflows, customize them with parameters, and generate user-friendly workflow reports—combining theory with practical application.

• Tuesday: Workflow FAIRification, Documentation, and Export

  Begin with a recap of Day 1, then explore UseGalaxy.fr and its unique features. Learn to annotate workflows with metadata, apply best practices for FAIR compliance, and implement tests to ensure reliability. Publish your workflows to WorkflowHub and Dockstore via the IWC. Develop high-resolution workflow visualizations and create interactive tutorials using a “Choose Your Own Tutorial” approach. Finally, master workflow export by creating RO-Crates for reproducibility and submitting workflows to LifeMonitor for performance tracking.

• Wednesday: Scaling Workflows & Galaxy Using Command-Line and API

  Start with a recap and real-world examples of large-scale Galaxy projects. Learn to execute workflows from the command line using Planemo, automate batch processing with shell scripts, and analyze performance for efficiency. Discover how to scale Galaxy use with BioBlend, designing Python scripts for batch workflow execution and evaluating scalability. The day concludes with an introduction to the “Bring Your Own Work” session.

• Thursday: Bring Your Own Work (BYOW)

  Dedicate the day to applying your new skills to your own projects. With guidance from trainers, refine your workflows, troubleshoot challenges, and implement solutions using your personal data. Collaborate with peers, document your progress, and optimize your workflows to leave with actionable results for your research.

• Friday: Storage, Data Management, Recap, and Closing

  The final half-day begins with a recap of the week’s progress, followed by a session on “Bring Your Own Storage”, exploring how to integrate personal or institutional storage with Galaxy. Learn about managing databases in Galaxy and the IDC (Intergalactic Data Commission) effort for efficient data organization. The workshop concludes with a general recap, supplementary exercises, and feedback and closing remarks, ensuring you leave with a comprehensive understanding and resources for continued success.

This training will be conducted in French, while the materials (slides) will be in English.

Learning Objectives

At the end of the workshop, you will be able to:

• Workflow development
  • Understand the key aspects of workflows by identifying their core components and purpose.
  • Create clean, non-repetitive workflows by applying best practices for process design.
  • Use workflow parameters to customize and optimize workflows for specific tasks.
  • Generate user-friendly workflow reports to display workflow results in a structured way.
• Workflow FAIRyfication
  • Annotate a Galaxy workflow with essential metadata to ensure it is findable and reusable.
  • Apply best practices to data analysis workflows to improve consistency and interoperability.
  • Implement robust tests to validate workflow reliability and accuracy.
  • Publish a Galaxy workflow on WorkflowHub and Dockstore via its integration into the IWC, demonstrating enhanced findability, accessibility, interroperability and usability for the scientific community.
• Workflow Documentation
  • Design a high-resolution workflow image optimized for documentation and presentations.
  • Develop a hands-on tutorial with a “Choose Your Own Tutorial” approach, including:
    • A step-by-step tutorial with skeleton generation from the workflow.
    • A real-time tutorial that runs and explains the workflow interactively.
  • Produce a final documentation package that includes both tutorial formats and high-resolution visuals.
• Workflow Export
  • Apply the process of creating a Galaxy Workflow Run RO-Crate by packaging a workflow with its metadata, inputs, and outputs, ensuring it is reproducible and FAIR-compliant.
  • Evaluate the completeness and accuracy of a Galaxy Workflow Run RO-Crate by reviewing its structure, metadata, and included files for adherence to best practices.
  • Submit a workflow to LifeMonitor, analyzing the platform’s feedback to assess workflow performance and improve its reliability for future use.
• Workflow Scaling using command-line
  • Execute workflows from the command line using the Planemo run subcommand, demonstrating the ability to run and monitor workflows outside the Galaxy interface.
  • Develop simple shell scripts to automate the execution of multiple workflows concurrently or sequentially, optimizing efficiency and scalability.
  • Analyze the performance and resource usage of workflows run via shell scripts, evaluating the effectiveness of scaling strategies for large-scale data processing.
• Scaling Galaxy Use with the API and BioBlend
  • Utilize the BioBlend library to programmatically interact with Galaxy, executing workflows, managing datasets, and automating repetitive tasks.
  • Design a Python script using BioBlend to scale Galaxy workflows for batch processing, ensuring efficient resource use and reproducibility.
  • Evaluate the performance and scalability of workflows executed via BioBlend, comparing results with manual Galaxy interactions to identify improvements.
• “Bring Your Own Work”
  • Apply the concepts and tools learned during the training to develop or refine your own workflows using your personal data, with guidance from trainers.
  • Troubleshoot challenges in your workflow or data analysis, implementing solutions with the support of trainers and peers.
  • Demonstrate progress in your project by documenting your workflow, results, and any optimizations made during the sessions.

Requirements

• Prior knowledge and experience using Galaxy
• Prior knowledge and experience using command line
• Fluent in French (materials will be in English and discussions will happen in French)

Registration

This in-person-only workshop is limited to 20 participants to ensure personalized attention and hands-on support. The course will proceed with a minimum of 10 registrations. Registration will open in April 2026—stay tuned for updates!

Who is this course for?

This course is designed for data scientists, advanced Galaxy users, and team leaders who need to scale up their data analysis workflows for batch processing, automation, or production-level applications. Whether you’re looking to optimize workflows, integrate external tools, or enhance reproducibility and scalability, this training will provide the skills to leverage Galaxy effectively. The sessions will be conducted in French, while the training materials (slides) will be in English.

Event Location

Geocoding via Nominatim, Map data from OpenStreetMap

Organisers & Instructors

This event is brought to you by:

Organiser(s)	Anthony Bretaudeau Bérénice Batut Gildas Le Corguillé Solenne Correard Marie Josse Laura Leroi Loraine Guéguen Clea Siguret Romane LIBOUBAN Fabien Mareuil
Instructor(s)	Anthony Bretaudeau Bérénice Batut Gildas Le Corguillé Solenne Correard Marie Josse Laura Leroi Romane LIBOUBAN Fabien Mareuil

IFB