Skip to content
2021-online
Switch branches/tags
Go to file
Code

Files

Permalink
Failed to load latest commit information.

README.md

Galaxy Admin Training logo: GTN star over center of a galaxy background with the text Galaxy Admin Training

logo based on a Hubble Image

Galaxy Administration Training

Location, Logistics

This training is offered Online, January 25-29, and is mostly asynchronous. Throughout the week you will always have access to trainers that are ready to help you with tasks or understanding. However the bulk of the work consist of you working at your own pace through the materials we prepared for you.

For the duration of this training (and a week after) you'll be granted access to a virtual machine (VM) that will be exclusive to you. You will connect to it using ssh ubuntu@address-of-your-machine and perform all of training's tasks inside. The machine is configured in a way to allow trainers connect to your machine and see exactly what you see. For this it uses software called byobu that has many convenient features for working in terminal - you can check out our byobu help page.

Important Links

Timetable

The course is a mix of:

  1. video recorded by our instructor community
  2. video auto-generated from our slides
  3. tutorials without videos.

We've done this to balance the significant effort required to produce videos for materials that are regularly updated with the potential benefits they will have for you, the students. As a result you'll find more videos for the extremely important, foundational topics where we wanted things to be completely clear for you.

If you do not like videos: The videos are strictly supplementary to the training material and will show instructors going through the lessons. If you prefer video content, you can watch those. If you dislike video training, you can choose to just read the training materials for each topic.

The schedule for each day is a suggestion of what we believe is approximately 5 hours of work.

  • If you're done with a day and want to do more, please feel free to continue!
  • If you can't complete everything at the same pace, that's also fine! The VMs will be available for a week after the event.

CoC

Everyone is expected to abide by the Galaxy Code of Conduct (CoC). We want this to be a welcoming and friendly environment for everyone! Please see the CoC for more information and the point of contact for any issues.

Monday

This day covers getting a Galaxy server setup with Ansible, a server you will develop for the rest of the week.

Start today by introducing yourself in the #general channel in Slack! Tell us where you're from, and and one thing about your surroundings (e.g. it's snowing outside, there's a squirrel on my porch, my cat is on my keyboard)

Topic Video Slides / Materials Slack Channel
Welcome and introduction Video #general
Intro to Ansible Video Slides #01-ansible
Ansible Video Tutorial #01-ansible
Galaxy Ansible Introduction Video Slides #02-ansible-galaxy
Part 0: Playbook Overview Video[1] Tutorial part 0 #02-ansible-galaxy
Part 1: Basic Installation Video[1] Tutorial part 1 #02-ansible-galaxy
Database Video[1] Slides #02-ansible-galaxy
SystemD Video[1] Slides #02-ansible-galaxy
Part 2: Towards Production Video[1] Tutorial part 2 #02-ansible-galaxy
Production Video[1] Production #02-ansible-galaxy
Part 3: Advanced Install Video[1] Tutorial part 3 #02-ansible-galaxy
uWSGI Slides #02-ansible-galaxy
Touch Base Telco (See Slack)
  1. The same videos at different timepoints.

Tuesday

Start today by sharing how your 5-year-old self would have finished this sentence? “When I grow up, I want to be …”? in the #general channel in Slack!

Topic Video Slides / Materials Slack Channel
Running jobs in Singularity Video Tutorial #03-singularity
Ephemeris (Intro) Video[1] Slides #03-ephemeris
Ephemeris Video[1] Tutorial #03-ephemeris
Users, Groups, and Quotas Video Slides #general
Reference Data (Intro) Video Slides #04-cvmfs
Reference Data Video Tutorial #04-cvmfs
Data Libraries Video Tutorial #05-data-libraries
BioBlend (Intro) Video Slides #06-bioblend
BioBlend Video[2] Tutorial #06-bioblend
Touch Base Telco (See Slack)
  1. The same videos at different timepoints.
  2. The BioBlend tutorial was recorded during BCC2020. It mentions "Remo" numerous times which was the platform for that conference. You can safely ignore these portions, but the demonstration of the notebooks is still valid and useful.

Wednesday

Start today by sharing what is your recent favorite tool or app or software in the #general channel in Slack.

Topic Video Slides / Materials Slack Channel
Galaxy Cluster Computing (Intro)¶ Video Slides #07-compute-cluster
Connecting Galaxy to a compute cluster Video Tutorial #07-compute-cluster
Mapping Jobs to Destinations Video Tutorial #07-compute-cluster
Recording Job Metrics Video Tutorial #07-compute-cluster
Touch Base Telco (See Slack)

Thursday

Start today by sharing What has been your favourite thing about the course so far? in the #general channel in Slack.

Topic Video Slides / Materials Slack Channel
Pulsar (Intro) Video Slides #08-pulsar
Pulsar Video Exercise #08-pulsar
Storage management Video 1, Video 2 Exercise #09-storage
DB Query (Intro) Video Slides #09-storage
DB queries, command line & scripts Exercise #09-storage
Monitoring (Intro) Video Slides #10-monitoring
Monitoring: Telegraf, InfluxDB, Grafana¶ Video Telegraf Exercise #10-monitoring
Maintenance, Backup and Restore Video Slides #10-monitoring
Touch Base Telco (See Slack)

Friday

Start today by sharing What music/artist/audiobook have you been listening to these days? in the #general channel in Slack.

Today is a "Choose Your Own Adventure" day. Choose the content you're interested in, and we'll be around to support you.

Topic Video Slides / Materials Slack Channel
What's new in Galaxy Slides: 2019, 2020 #11-cyoa
Training Infrastructure as a Service (TIaaS)¶ Video TIaaS Exercise #12-tiaas
Monitoring With Reports Reports Exercise #10-monitoring
Interactive Tools Video Slides, Exercise #11-cyoa
Jenkins & Automation Exercise #11-cyoa
Advanced Customisation Slides #11-cyoa
When things go wrong: Galaxy Server Troubleshooting Slides #11-cyoa
Python 2 to Python 3! Docs #11-cyoa
Tool Development Slides, Exercise #11-cyoa
Dataset Collections DCs, Rule based #11-cyoa
Developing your own Training Setting up, Exercise #11-cyoa
Securing your Galaxy¶ Video Their team is not releasing these until February 2. #11-cyoa
Touch Base Telco (See Slack)

¶: These videos do not currently have corrected captions, only automated ones.

Instructors

Name Country Affiliation(s)
Helena Rasche NL Erasmus MC Bioinformatics Group, ATGM, Avans Hogeschool Breda
Nicola Soranzo UK Earlham Institute
Martin Čech CZ Elixir Czech Republic, RECETOX
Anthony Bretaudeau FR GenOuest, BIPAA
Estelle Ancelet FR INRAE
Sergey Golitsynskiy US Johns Hopkins University
Gianmauro Cuccuru DE Albert-Ludwigs-University Freiburg
Saskia Hiltemann NL Erasmus MC Bioinformatics Group
Gildas Le Corguillé FR ABiMS - Sorbonne Université/CNRS, IFB/ELIXIR-FR
Simon Gladman AU Melbourne Bioinformatics - Galaxy Australia
Catherine Bromhead AU Melbourne Bioinformatics - Galaxy Australia
David Morais CA GenAP & Compute Canada
Aaron Petkau CA PHAC & University of Manitoba

(others coming soon.)

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.

Training VM instances

Galaxy training instances are bootstrapped with a small Ansible playbook, which you may find useful for repeating the exercises later using a VM, Docker image, etc.

Sponsors

The 2021 Galaxy Admin Training is sponsored by a wide variety of organisations

EOSC Life

This course has received funding from EOSC-Life Second Training Open Call. EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087

EOSC Life logo

Jetstream

We are grateful to Jetstream and the Galaxy Team for providing VMs from their allocation TG-CCR160022 for this event.

Jetstream logo, it's dark red lettering with a teal green wave in an affront to good design

Galaxy Australia & Australian BioCommons

A significant portion of our infrastructure was graciously provided by Galaxy Australia

Australian BioCommons

de.NBI

Virtual Machines were provided by the German Federal Ministry of Education and Research BMBF grant 031 A538A de.NBI-RBC.

de.NBI Logo