dagobah - The Solar System for Galaxy Training
"The planet shown in Dagobah, in the Sluis sector, is a world of murky swamps, steaming bayous, and petrified forests."
Melbourne - 6th to 9th February 2017
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Built slides have an index.
- (N)ate Coraor - Galaxy Project, BMB, Penn State University, USA
- (S)imon Gladman - VLSCI, University of Melbourne, Australia
- (E)nis Afgan - Galaxy Project, Department of Biology, Johns Hopkins University, USA
- (B)jörn Grüning - Head of Freiburg Galaxy Team, University of Freiburg, Germany
- (R)oss Lazarus - Galaxy Project and formerly of Baker IDI, Australia.
List of instances for course:
6th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 08:30 | Registration | ||
| 09:15 | Welcome and introduction | Slides | All |
| 09:30 | Deployment and platform options | Slides | (N) |
| 10:00 | Get a basic Galaxy server up and running | Slides | (N) + (E)?) |
| 10:45 | Morning break | ||
| 11:00 | Galaxy server optional necessities: PostgreSQL and nginx | First Steps Slides, First Steps Exercise, PostgreSQL Slides, PostgreSQL Exercise, nginx/Apache Slides, nginx Exercise, Apache Exercise (for reference) | (N) + (E) |
| 12:15 | Lunch | ||
| 13:00 | Galaxy server optional necessities (continued) | ||
| 13:45 | Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools | Slides (Shed), Slides (Tools), Slides (Dependencies), Exercise | (B) |
| 15:00 | Afternoon break | ||
| 15:15 | Defining and importing genomes, Data Managers | Slides, Exercise | (S) |
| 16:50 | Extending your installation: FTP, SMTP, and more | Slides, Exercise | (N) |
| 18:00 | Close Day 1 | All |
7th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09:15 | Users, Groups, and Quotas | Slides | (S) |
| 10:30 | Upgrading to a new Galaxy release | Slides | (E) + (R)? |
| 11:00 | Morning break | ||
| 11:15 | Updating tools and supporting multiple versions of tools | Exercise | (B) |
| 12:30 | Lunch | ||
| 13:15 | Improving the web serving experience with uWSGI | Slides Exercise | (N) |
| 14:15 | Controlling Galaxy with systemd and supervisor | Slides, Exercise | (N) |
| 15:15 | Afternoon break | ||
| 15:30 | Server monitoring and maintenance: Admin UI, Log files, Direct database queries, command line & scripts, what to backup and how | Slides, Exercise | (S) + (N) |
| 16:30 | Using and configuring external authentication services | Slides, PAM Auth Exercise, Upstream Auth Exercise | (N) |
| 17:45 | Questions and ad-hoc troubleshooting | All | |
| 18:00 | Close Day 2 | All |
8th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09:15 | Configuration management choices: Introduction to Ansible | Slides, Exercise | (S) |
| 10:00 | Using Ansible to deploy Galaxy I | Exercise | (S) |
| 10:30 | Morning break | ||
| 10:45 | Using Ansible to deploy Galaxy II | (S) + (N) | |
| 12:20 | Lunch | ||
| 13:05 | Exploring the Galaxy job configuration file | Slides | (N) |
| 13:50 | Connecting Galaxy to a compute cluster I | Slides, Exercise 1, Exercise 2 | (N) |
| 15:30 | Afternoon break | ||
| 15:45 | Connecting Galaxy to a compute cluster II | (N) | |
| 16:30 | Using heterogeneous compute resources | Slides, Exercise | (N) |
| 17:30 | Using public and private cloud compute resources | Slides | (E) |
| 18:00 | Close day 3 | All |
We will most likely all go out for dinner together somewhere local tonight
9th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09:15 | Storage management and using heterogeneous storage services | Slides, Exercise | (N) |
| 10:30 | Morning break | ||
| 10:50 | Containerize all the things: Galaxy in Docker and Docker in Galaxy | Docker Slides Conda Slides | (B) |
| 12:30 | Lunch | ||
| 13:15 | Running Jupyter in Galaxy with Galaxy Interactive Environments | Exercise | (B) + (N) |
| 14:30 | When things go wrong: Galaxy Server Troubleshooting | Slides | (N) |
| 15:30 | Afternoon break | ||
| 15:45 | OPEN: Submitted topics | link to nomination document, uWSGI Zerg Mode | |
| 16:45 | Galaxy server architecture | Slides | |
| 18:00 | Wrap up and close | All |