Intro to Galaxy Administration @ Pennsylvania State University
Monday 1/28/2019 - Friday 2/1/2019
Location
Room W306, Millennium Science Complex - map Penn State University, State College, Pennsylvania, USA
Training VM instances
We are using instances from the Jetstream cloud with 2 cores, 4 GiB memory, 20 GiB disk, running a minimal Ubuntu 18.04 image
The instances have been bootstrapped with a small Ansible playbook, which you may find useful for repeating the exercises at home using a VM, Docker image, etc.
Timetable
Timetable with sessions and material is being continuously updated.
Monday
28th January
| 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 | S |
| 10:30 | Break (coffee & snacks) | |||
| 10:45 | Galaxy Server Part 1: Basic Install | Database, uWSGI | Exercise | H |
| 12:30 | Lunch (catered) | |||
| 13:30 | Galaxy Server Part 2: Towards Production | NGINX, Supervisor | H | |
| 15:30 | Break (coffee & snacks) | |||
| 15:50 | Galaxy Server Part 3: Advanced Install | Production | H | |
| 17:00 | Close Day 1 |
Tuesday
29th January
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Galaxy Tool Shed | Tools, Toolshed | H, S, M | |
| 10:00 | Ephemeris | Ephemeris | Exercise | J, M |
| 10:30 | Break (coffee & snacks) | |||
| 10:50 | Ephemeris: Continued | M, H | ||
| 12:00 | Lunch (catered) | |||
| 13:00 | Users, Groups, and Quotas | Slides | M | |
| 14:00 | Reference Data | Slides | Exercise, CMVFS Exercise | S |
| 16:15 | External authentication | Slides | Upstream Auth Exercise | H |
| 17:00 | Close Day 2 |
Wednesday
30th January
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Exploring the Galaxy job configuration file | Slides | J | |
| 09:45 | Connecting Galaxy to a compute cluster | Slides | Exercise | N, H |
| 10:20 | Break (coffee & snacks) | |||
| 10:40 | Compute cluster (continued) | |||
| 12:00 | Lunch (on your own) | |||
| 13:30 | Using heterogeneous compute resources | Slides | Exercise | S, N |
| 15:15 | Break (coffee & snacks) | |||
| 15:35 | compute resources continued | |||
| 17:00 | Close day 3 |
Thursday
31th January
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Compute Resources: Continued (Job Resources) | N | ||
| 10:45 | Break (coffee & snacks) | |||
| 11:00 | Containerize all the things: Galaxy in Docker and Docker in Galaxy | Docker Slides | J | |
| 12:00 | Lunch (catered) | |||
| 13:00 | Cloudbursting showcase | Cloud slides | S | |
| 13:30 | Storage management | Slides | Exercise | M, S |
| 14:30 | Server Monitoring and Maintenance Part 1: Telegraf, InfluxDB, Grafana | Slides | Telegraf Exercise Reports Exercise | M, H |
| 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 |
Friday
1st February
| Time | Topic | Slides | Exercises | Instructor |
|---|---|---|---|---|
| 09:00 | Welcome and questions | |||
| 09:15 | Dockerizing a Galaxy Tool | Exercise | J | |
| 10:00 | Break (coffee & snacks) | |||
| 10:15 | What's new in Galaxy? | Slides | N, J | |
| 10:40 | Upgrading Galaxy | Slides | M | |
| 11:00 | Telegraf | Exercise | H | |
| 11:30 | gxadmin | Exercise | H | |
| 11:50 | Empathy | Slides | H | |
| 12:00 | Lunch (catered) | |||
| 13:00 | When things go wrong: Galaxy Server Troubleshooting | Slides | N | |
| Spare Time | Extra Topics | Slides | S | |
| 15:00 | Wrap up and close |
Instructors
- (S)imon Gladman - Melbourne Bioinformatics, University of Melbourne, Australia
- (H)elena Rasche - ELIXIR Galaxy WG, Elixir Germany, de.NBI, University of Freiburg, Germany
- (N)ate Coraor - Galaxy Project, Penn State University, USA
- (J)ohn Chilton - Galaxy Project, Penn State University, USA
- (M)artin Čech - Galaxy Project, Penn State University, USA
