2-6 March 2020
This training will be offered 2-6 March at the Barcelona Supercomputing Center.
See the workshop's Galaxy Community Hub page for details on logistics and registration.
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.
Timetable with sessions and material is being continuously updated. This is NOT final.
This day covers getting a Galaxy server setup with Ansible, a server you will develop for the rest of the week.
2nd March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 08:30 | Registration | |||
| 09:00 | Welcome and introduction | Welcome | All | |
| 09:20 | Deployment and platform options | Deployment | M | |
| 09:40 | Intro to Ansible | Ansible | Exercise | Ni |
| 10:30 | Break (coffee & snacks) | |||
| 10:45 | Galaxy Server Part 1: Basic Install | Galaxy Install, Database, uWSGI | Exercise | H, M, Na |
| 12:00 | Lunch (catered) | |||
| 13:00 | Galaxy Server Part 2: Towards Production | systemd | H, Na | |
| 14:00 | Break (coffee & snacks) | |||
| 15:15 | Galaxy Server Part 3: Advanced Install | Production | H, Na | |
| 15:45 | Galaxy Tool Shed | Toolshed | M | |
| 16:15 | Ephemeris | Ephemeris | Exercise | Ni |
| 17:00 | Guided tour of the Supercomputing facility |
3rd March
Today we pivot to focus on making that server useful: adding tools and data, configuring quotas and authentication
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Ephemeris: Continued | |||
| 10:30 | Break (coffee & snacks) | |||
| 10:45 | Users, Groups, and Quotas (+Demo) | Slides | S | |
| 12:30 | External authentication | Slides | Upstream Auth Exercise | H |
| 13:00 | Lunch (catered) | |||
| 14:00 | Reference Data | Slides | CVMFS Exercise, Data Manager Exercise | Na |
| 15:00 | Exploring the Galaxy job configuration file | Slides | job_conf.xml |
M |
| 15:45 | Connecting Galaxy to a compute cluster | Slides | Exercise | Na |
| 17:00 | Close Day 2 |
4th March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Connecting Galaxy to a compute cluster (continued) | Slides | Exercise | Na |
| 10:45 | Break (coffee & snacks) | |||
| 11:00 | BioBlend | Slides | Exercise | Ni |
| 12:00 | Pulsar | Slides | Exercise | H |
| 13:00 | Lunch (catered) | |||
| 14:00 | Storage management | Exercise | H | |
| 15:00 | Monitoring Part 1: Reports | Reports Exercise | M | |
| 15:30 | Break (coffee & snacks) | |||
| 15:45 | Monitoring Part2: DB queries, command line & scripts | Slides | gxadmin | H |
| 16:15 | Monitoring Part 3: Telegraf, InfluxDB, Grafana | Slides | Telegraf Exercise | S |
| 17:00 | Close day 3 |
5th March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Monitoring Part 3: Telegraf, InfluxDB, Grafana (continued) | Slides | Telegraf Exercise | S |
| 10:15 | Maintenance, Backup and Restore | Slides | Na | |
| 10:45 | Break (coffee & snacks) | |||
| 11:00 | TIaaS | TIaaS Exercise | H & S | |
| 12:30 | Recording Job Metrics | Exercise | Na | |
| 12:45 | Interactive Tools | Slides | Exercise | Na |
| 13:00 | Lunch | |||
| 14:00 | Interactive Tools | Slides | Exercise | Na |
| 15:00 | Dev vs Prod | (Conversation) | Na | |
| 15:30 | Break (coffee & snacks) | |||
| 15:45 | Jenkins & Automation | Exercise | H | |
| 16:35 | Advanced Customisation | Slides | H | |
| 17:00 | Wrap up and close |
6th March
The last day! We made it. Today we have some additional topics, some of which are not admin related. Please feel free to leave at any point in the day and go enjoy Barcelona if the topics are maybe a bit less interesting for you.
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | When things go wrong: Galaxy Server Troubleshooting | Slides | Na | |
| 10:45 | Break (coffee & snacks & survey) | |||
| 11:00 | What's new in Galaxy | Slides | M | |
| 11:45 | Python 2 to Python 3! | Docs | Ni | |
| 12:00 | Tool Development | Slides | Exercise | Ni |
| 13:00 | Lunch (catered) | |||
| 14:00 | Dataset collections | DCs, Rule based | M | |
| 14:30 | Developing your own Training | Setting up, Exercise | S | |
| 15:00 | Wrap up and close |
- (H)elena Rasche - Galaxy Europe
- (S)askia Hiltemann - Erasmus Medical Center, the Netherlands
- (Na)te Coraor - Galaxy Project, Penn State University, United States
- (M)arius van den Beek - Galaxy Project, Penn State University, Europe
- (Ni)cola Soranzo - Earlham Institute