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.
2nd March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 08:30 | Registration | |||
| 09:00 | Welcome and introduction | Welcome | All | |
| 09:20 | Deployment and platform options | Deployment | ||
| 09:40 | Intro to Ansible | Ansible | Exercise | |
| 10:30 | Break (coffee & snacks) | |||
| 10:45 | Galaxy Server Part 1: Basic Install | Database, uWSGI | Exercise | |
| 12:30 | Lunch (catered) | |||
| 13:30 | Galaxy Server Part 2: Towards Production | NGINX, Supervisor | ||
| 15:30 | Break (coffee & snacks) | |||
| 15:50 | Galaxy Server Part 3: Advanced Install | Production | ||
| 17:00 | Close Day 1 |
3rd March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Galaxy Tool Shed | Tools, Toolshed | ||
| 10:00 | Ephemeris | Ephemeris | Exercise | |
| 10:30 | Break (coffee & snacks) | |||
| 10:50 | Ephemeris: Continued | |||
| 12:00 | Lunch (catered) | |||
| 13:00 | Users, Groups, and Quotas | Slides | ||
| 14:00 | Reference Data | Slides | Exercise, CMVFS Exercise | |
| 16:15 | External authentication | Slides | Upstream Auth Exercise | |
| 17:00 | Close Day 2 |
4th March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Exploring the Galaxy job configuration file | Slides | ||
| 09:45 | Connecting Galaxy to a compute cluster | Slides | Exercise | |
| 10:20 | Break (coffee & snacks) | |||
| 10:40 | Compute cluster (continued) | |||
| 12:00 | Lunch (on your own) | |||
| 13:30 | Using heterogeneous compute resources | Slides | Exercise | |
| 15:15 | Break (coffee & snacks) | |||
| 15:35 | compute resources continued | |||
| 17:00 | Close day 3 |
5th March
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Compute Resources: Continued (Job Resources) | |||
| 10:45 | Break (coffee & snacks) | |||
| 11:00 | Containerize all the things: Galaxy in Docker and Docker in Galaxy | Docker Slides | ||
| 12:00 | Lunch (catered) | |||
| 13:00 | Cloudbursting showcase | Cloud slides | ||
| 13:30 | Storage management | Slides | Exercise | |
| 14:30 | Server Monitoring and Maintenance Part 1: Telegraf, InfluxDB, Grafana | Slides | Telegraf Exercise Reports Exercise | |
| 15:15 | Break (coffee & snacks) | |||
| 15:30 | Server Monitoring and Maintenance Part 2: DB queries, command line & scripts, backup | gxadmin | ||
| 17:00 | Wrap up and close |
6th MArch
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Dockerizing a Galaxy Tool | Exercise | ||
| 10:00 | Break (coffee & snacks) | |||
| 10:15 | What's new in Galaxy? | Slides | ||
| 10:40 | Upgrading Galaxy | Slides | ||
| 11:00 | Telegraf | Exercise | ||
| 11:30 | gxadmin | Exercise | ||
| 11:50 | Empathy | Slides | ||
| 12:00 | Lunch (catered) | |||
| 13:00 | When things go wrong: Galaxy Server Troubleshooting | Slides | ||
| Spare Time | Extra Topics | Slides | ||
| 15:00 | Wrap up and close |
- (H)elena Rasche -
- (S)askia Hiltemann -
- (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
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