Martin Čech -- 26.3.25 -- FI:PV269 Pokročilé metody bioinformatiky -- ELIXIR CZ / CESNET
- 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 it's all at https://training.galaxyproject.org/
- 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:
- Planemo
- vscode Language server
- Interactive tools:
- Reproducible Scientific Workflows With Galaxy https://bit.ly/sciflows
- Vertebrate Genomes Project https://bit.ly/galaxy-elixir24
- set of trainig materials for bycovid project
- showcase of vetted & tested tools: https://iwc.galaxyproject.org/
- covid variant calling
- covid project results:
- expression tools and workflow parameters
- automation of workflows from cli training
- Collections & Rule Based Uploader
- 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
- 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
- Ansible for Infrastructure As A Code
- Gravity: supervisor for Galaxy process management (wrapper for systemd/supervisor)
- wrap a tool: https://github.com/martenson/galaxy-tool-task/
- upload solution to is.muni