Martin Čech -- 25.3.26 -- UPOL:Bioinformatika v Galaxy -- UOCHB / ELIXIR CZ / CESNET martin.cech@cesnet.cz
- For Galaxy's web interface the target audience is a bench scientist.
- The assumption is that in the future it could also be your audience as bioinformaticians.
- We'll look into what Galaxy provides you with in order to make your job easier.
- Galaxy provides a simplified interface to software and compute infrastructure. Strives to be domain-agnostic.
- https://bit.ly/gxy_intro
- Intro slides
- hands-on at https://usegalaxy.cz
- https://training.galaxyproject.org/topics/sequence-analysis/tutorials/quality-control/tutorial.html
| Concept | Why It Matters |
|---|---|
| Provenance & Reproducibility | The History automatically records tool version, parameters, and input dataset IDs. |
| FAIR & Open Science | Galaxy encourages sharing datasets, workflows, and results with DOIs, satisfying journal & funder mandates. |
| Scalability | Jobs can be dispatched to local clusters, cloud nodes, or a Galaxy “worker” queue – transparent to the user. |
| ToolShed & Community‑built Wrappers | Thousands of tools are already available; you never have to reinvent a bowtie2 wrapper. |
| Interactive Environments | Jupyter & RStudio inside Galaxy give you the best of both worlds (code + UI). |
| Automation via API | Python client (bioblend) can drive Galaxy from scripts – essential for large batch processing. |
| Containerisation (Docker/Singularity) | All Galaxy tools run inside conda environments; Galaxy also supports Docker images for reproducible deployment. |
| Workflow Editing & Sub‑workflows | Complex pipelines can be modularised (e.g., separate QC sub‑workflow). |
| Versioning & Continuous Integration | Galaxy tools are tested automatically on the ToolShed CI – ensures reliability. |
| Teaching & Collaboration | Use Galaxy as a “lab notebook” for courses; students can share histories and comment on analyses. |
- 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:
- Vertebrate Genomes Project slides
- set of trainig materials for bycovid project
- showcase of vetted & tested workflows: 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)
If you take one thing from here be it that all the things are at training.galaxyproject.org
- wrap a tool: https://github.com/martenson/galaxy-tool-task/