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Galaxy Administration Training
Location, Logistics, and Registration
This training will be offered Online, January 25-29
Training VM instances
Galaxy training instances will be bootstrapped with a small Ansible playbook, which you may find useful for repeating the exercises at home using a VM, Docker image, etc.
Important Links
- https://gxy.io/gat-questions - Q&A!
- https://gxy.io/gatchat - Chat for this workshop
- https://gxy.io/gatmachines - VMs
Timetable
Timetable with sessions and material is being continuously updated. This is NOT final.
Monday
This day covers getting a Galaxy server setup with Ansible, a server you will develop for the rest of the week.
| Topic | Slides | Exercises |
|---|---|---|
| Registration | ||
| Welcome and introduction | Welcome | |
| Deployment and platform options | Deployment | |
| Intro to Ansible | Ansible | Exercise |
| Galaxy Server Part 1: Basic Install | Galaxy Install, Database, uWSGI | Exercise |
| Galaxy Server Part 2: Towards Production | systemd | |
| Galaxy Server Part 3: Advanced Install | Production |
Tuesday
| Topic | Slides | Exercises |
|---|---|---|
| Galaxy Tool Shed | Toolshed | |
| Ephemeris | Ephemeris | Exercise |
| Users, Groups, and Quotas (+Demo) | Slides | |
| Reference Data | Slides | CVMFS Exercise, Data Manager Exercise |
| BioBlend | Slides | Exercise |
Wednesday
| Topic | Slides | Exercises |
|---|---|---|
| Exploring the Galaxy job configuration file | Slides | job_conf.xml |
| Connecting Galaxy to a compute cluster | Slides | Exercise |
| Recording Job Metrics | Exercise |
Thursday
| Topic | Slides | Exercises |
|---|---|---|
| Pulsar | Slides | Exercise |
| Storage management | Exercise | |
| Monitoring Part 1: DB queries, command line & scripts | Slides | gxadmin |
| Monitoring Part 2: Telegraf, InfluxDB, Grafana | Slides | Telegraf Exercise |
| Maintenance, Backup and Restore | Slides |
Friday
Today is a "Choose Your Own Adventure" day. Choose the content you're interested in, and we'll be around to support you.
| Topic | Slides | Exercises |
|---|---|---|
| Monitoring With Reports | Reports Exercise | |
| TIaaS | TIaaS Exercise | |
| Interactive Tools | Slides | Exercise |
| Jenkins & Automation | Exercise | |
| Advanced Customisation | Slides | |
| When things go wrong: Galaxy Server Troubleshooting | Slides | |
| What's new in Galaxy | Slides | |
| Python 2 to Python 3! | Docs | |
| Tool Development | Slides | Exercise |
| Dataset collections | DCs, Rule based | |
| Developing your own Training | Setting up, Exercise |
Instructors
After the Training
Everything you were taught in the past few days can be found in the Galaxy Admin Training repository, which mostly points to the admin section of the Galaxy Training Materials.
For those of you who also need to do some Galaxy development, there is a dev section of training materials for those topics as well. There you can learn to integrate webhooks and tours, and learn about advanced tool development. For those who need to teach Galaxy or want to contribute training materials, we have lots of tutorials for you!
Community
Chat with us on Gitter!
For your Users
We recommend setting the helpsite_url in your Galaxy configuration to point to https://help.galaxyproject.org/ where users can go and chat with each other. It's a great resource to help your users be independent and self-sufficient in their Galaxy learning. Admins are welcome too!
And don't forget that many, many training materials already exist covering different areas of *omics and other research done with Galaxy. This can be a great resource for either giving training courses to your users (join the train-the-trainer session at GCC if you want to learn more) or to just point users to as a self-directed learning resource.
If you're asked to provide training infrastructure for your users, but do not have the capacity to support this, UseGalaxy.eu provides training infrastructure for free.
Going Forward
We are working on updating the training materials with feedback from the training, and looking into the possibility to develop some automated linting of configurations, to help make Galaxy deployment more error-proof.
Let us know if you have any questions or feedback! Chat on Gitter, file issues on GitHub, let us know what features are interesting and important to the admin community.
