fimuni_22_10_25.md

ces.net/galaxy

Advanced Galaxy Topics

Martin Čech -- 22.10.25 -- FI:PV269 Pokročilé metody bioinformatiky -- ELIXIR CZ / CESNET

What is the purpose of Galaxy for this group?

• for Galaxy web interface the target audience is a bench scientist
• the assumption is in the future that could also be your audience
• we'll look into what is behind the scenes to allow you using Galaxy in order to deliver a service

If you take one thing from here be it that all the things are at training.galaxyproject.org

Galaxy 101

• hands-on at https://usegalaxy.cz
• https://training.galaxyproject.org/topics/sequence-analysis/tutorials/quality-control/tutorial.html

Galaxy Tool Concepts

• XML files: https://usegalaxy.cz/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
• development repo
• Tool Shed
• Dependencies:
  • published in https://anaconda.org/bioconda/fastqc
    • bioconda channel
    • recipe
    • source for containers
• Planemo
• vscode Language server
• Interactive tools:
  • training
  • demo

Galaxy Workflow Development

• Vertebrate Genomes Project slides
• set of trainig materials for bycovid project
• showcase of vetted & tested workflows: https://iwc.galaxyproject.org/
• covid variant calling
  • iwc
  • source
  • dockstore
  • workflowhub
• covid project results:
  • https://www.infectious-diseases-toolkit.org/showcase/covid19-galaxy
  • https://galaxyproject.org/projects/covid19/
• expression tools and workflow parameters
• automation of workflows from cli training

Galaxy Advanced Usage Concepts

• Collections & Rule Based Uploader
  • basic
  • advanced
• Training Infrastructure As A Service
  • when running a workshop
  • https://training.galaxyproject.org/training-material/topics/admin/tutorials/tiaas/tutorial.html
  • available at .org .eu .cz

Galaxy Architecture

• schema buildup
• final schema
• frontend
  • Implemented in JavaScript (ES6) and Typescript
  • Built with webpack
  • Vue.js for component definitions
• API
  • openAPI https://usegalaxy.cz/api/docs
  • bioblend
  • can e.g. run custom/modified client, or run local client against remote Gxy
• backend
  • large Python project
  • plugin driven: https://training.galaxyproject.org/training-material/topics/dev/tutorials/architecture/slides.html#60
• Job Handling
  • running jobs in a cluster (e.g. PBS on Metacentrum)
  • Runners
  • Pulsar
  • Total Perspective Vortex
• Reference Data & CVMFS
  • https://bit.ly/galaxy-elixir24
  • https://training.galaxyproject.org/training-material/topics/admin/tutorials/cvmfs/slides.html#1

Galaxy Deployment

• Ansible for Infrastructure As A Code
  • month-worth of tutorials
• Gravity: supervisor for Galaxy process management (wrapper for systemd/supervisor)

Homework

• wrap a tool: https://github.com/martenson/galaxy-tool-task/
• upload solution to is.muni