CoCalc -- 2026-10-12-Advanced-Galaxy-Training.md

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Path: blob/main/events/2026-10-12-Advanced-Galaxy-Training.md
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---

layout: event
title: "Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability"

# external: "https://galaxyproject.org/events/2025-03-10-galaxy-workshop-freiburg/"

description: |
    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**.

cover-image: events/images/Galaxy_AGT2026.png
cover-image-alt: logo for the Advanced Galaxy Training

date_start: 2026-10-12
date_end: 2026-10-16


cost: 850-900 euros (To be confirmed)
audience: |
    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**.
contact_email: berenice.batut@france-bioinformatique.fr

# async: false
mode: onsite

registration:
  link: 
  deadline: 2026-05-31
  open: false

tags:
- galaxy-interface
- workflow
- command-line
- advanced

contributions:
    organisers:
        - abretaud
        - bebatut
        - lecorguille
        - scorreard
        - Marie59
        - lleroi
        - loraine-gueguen
        - clsiguret
        - rlibouba
        - fmareuil
    instructors:
        - abretaud
        - bebatut
        - lecorguille
        - scorreard
        - Marie59
        - lleroi
        - rlibouba
        - fmareuil
    #testing:
    funding:
        - ifb

location:
  name: Institut Pasteur
  address: 25-28 Rue du Dr Roux
  postcode: 75015
  city: Paris
  country: France
  geo:
    lat: 48.8408253
    lon: 2.3081039

infrastructure:
  tiaas: false
  servers:
    - server: https://usegalaxy.eu
      name: Galaxy EU
    - server: https://usegalaxy.fr
      name: Galaxy FR


program:
  - section: "Monday: Introduction & Workflow development" 
    description: |
      This half-day session starts with a **welcome, icebreaker, and participant introductions** to set a collaborative tone. It continues with a **brief overview of Galaxy** and its workflow capabilities, followed by an **introduction to workflow development**. Participants will **design clean, efficient workflows**, **customize them using parameters**, and **generate user-friendly workflow reports**—blending theory with hands-on practice.
    tutorials:
      - type: custom
        name: Welcome
        time: "14:00"
      - type: custom
        name: Icebreaking
        time: "14:15"
      - type: custom
        name: Participant presentation
        time: "14:30"
      - type: custom
        name: Galaxy overview
        time: "14:50"
      - type: custom
        name: Break
        time: "15:00"
      - type: custom
        name: Galaxy Workflow introduction
        time: "15:30"
      - name: workflow-editor
        topic: galaxy-interface
        time: "15:40"
      - name: workflow-parameters
        topic: galaxy-interface
        time: "16:10"
      - name: workflow-reports
        topic: galaxy-interface
        time: "16:25"
      - type: custom
        name: End of the day
        time: "17:00"

  - section: "Tuesday: Workflow FAIRification, documentation and export"
    description: |
      The second day begins with a **recap of the previous day's key concepts**, followed by an introduction to **UseGalaxy.fr** and its unique features. Participants will then dive into **Workflow FAIRification**, learning to annotate workflows with metadata, apply best practices for consistency, and implement tests to ensure reliability—culminating in publishing workflows to **WorkflowHub** and **Dockstore** via the IWC. The session continues with **Workflow Documentation**, where attendees will create high-resolution workflow images and develop interactive tutorials using a "Choose Your Own Tutorial" approach. Finally, the day covers **Workflow Export**, focusing on creating **RO-Crates** for reproducibility, evaluating their completeness, and submitting workflows to **LifeMonitor** for performance tracking—equipping participants with the skills to share, document, and monitor their workflows effectively.
    tutorials:
      - type: custom
        name: Recap of the previous day
        time: "9:00"
      - type: custom
        name: UseGalaxy.fr
        time: "9:15"
      - name: workflow-fairification
        topic: galaxy-interface
        time: "9:30"
      - type: custom
        name: Break
        time: "10:30"
      - name: workflow-fairification
        topic: galaxy-interface
        time: "11:00"
      - type: custom
        name: Lunch
        time: "12:00"
      - name: workflow-posters
        topic: galaxy-interface
        time: "13:30"
      - name: create-new-tutorial
        topic: contributing
        time: "14:00"
      - type: custom
        name: Break
        time: "15:00"
      - type: custom
        name: Overview of the RO-Crate concept and its implementations
        time: "15:30"
      - name: ro-crate-in-galaxy
        topic: fair
        time: "16:00"
      - name: ro-crate-submitting-life-monitor
        topic: fair
        time: "16:30"
      - type: custom
        name: End of the day
        time: "17:00"

  - section: "Wednesday: Scaling workflow and Galaxy using command-line"
    description: |
      The third day starts with a **recap of the previous sessions**, followed by inspiring examples of **large-scale projects using Galaxy** to showcase real-world applications. Participants will then explore **Workflow Scaling**, learning to **execute workflows from the command line** using Planemo and **automate batch processing** with shell scripts, while analyzing performance for efficiency. The session will also cover **Scaling Galaxy Use with BioBlend**, where attendees will **programmatically interact with Galaxy** using Python, design scripts for batch workflow execution, and evaluate scalability compared to manual processes—empowering them to optimize workflows for large-scale data analysis. The day will end with explanation of the "Bring Your Own Work".
    tutorials:
      - type: custom
        name: Recap of the previous day
        time: "9:00"
      - type: custom
        name: Big projects using Galaxy
        time: "9:15"
      - name: workflow-automation
        topic: galaxy-interface
        time: "9:30"
      - type: custom
        name: Break
        time: "10:30"
      - name: workflow-automation
        topic: galaxy-interface
        time: "11:00"
      - type: custom
        name: Lunch
        time: "12:00"
      - name: bioblend-api
        topic: dev
        time: "13:30"
      - type: custom
        name: Break
        time: "15:00"
      - name: bioblend-api
        topic: dev
        time: "15:30"
      - type: custom
        time: "16:00"
        name: Django to Galaxy?
        time: "16:30"
      - type: custom
        name: End of the day
        time: "17:00"
        
  - section: "Thursday: Bring Your Own Work (BYOW)"
    description: |
      The fourth day is dedicated to **"Bring Your Own Work"**, offering participants hands-on time to **apply the skills and tools** learned throughout the training to their own projects. With guidance from trainers, attendees will **refine their workflows**, **troubleshoot challenges**, and **implement solutions** using their personal data. The session encourages collaboration and peer support, allowing participants to **document their progress**, optimize their workflows, and showcase their results—ensuring they leave with practical, actionable outcomes for their research.
    tutorials:
      - type: custom
        name: Group work
        time: "9:00"
      - type: custom
        name: Break
        time: "10:15"
      - type: custom
        name: Group work
        time: "10:45"
      - type: custom
        name: Lunch
        time: "12:00"
      - type: custom
        name: Group work
        time: "13:30"
      - type: custom
        name: Break
        time: "15:00"
      - type: custom
        name: Group work
        time: "15:30"
      - type: custom
        name: Bring Your Own Work group recap
        time: "16:30"
      - type: custom
        name: End of the day
        time: "17:00"

  - section: "Friday: Storage, data, general recap, and supplementary exercises"
    description: |
      The final half-day begins with a **recap of the previous day's progress**, followed by an introduction to **"Bring Your Own Storage"**, exploring how to integrate personal or institutional storage solutions with Galaxy. Participants will then learn about **managing databases in Galaxy** and the **IDC (Intergalactic Data Commission) effort**, gaining insights into efficient data organization and accessibility. The session concludes with a **general recap**, supplementary exercises to reinforce key concepts, and **feedback and closing remarks**, ensuring participants leave with a comprehensive understanding and resources for continued success.
    tutorials:
      - type: custom
        name: Recap of the previous day
        time: "9:00"
      - type: custom
        name: Bring Your Own storage
        time: "9:30"
      - type: custom
        name: Managing databases in Galaxy and the IDC effort
        time: "9:45"
      - type: custom
        name: Break
        time: "10:00"
      - type: custom
        name: General recap & Supplementary exercises
        time: "10:30"
      - type: custom
        name: Feedback
        time: "11:30"
      - type: custom
        name: Closing remarks
        time: "11:45"
      - type: custom
        name: End of the workshop
        time: "12:00"

---

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!

Learning Objectives

Requirements

Registration

Product

Resources

Company