Monday 1/28/2019 - Friday 2/1/2019
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TBA, State College, Pennsylvania, USA
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2 cores, 4 GiB memory, and 20 GiB disk, Ubuntu 16.04
We are using instances from the Jetstream cloud, image ID acb53109-941f-4593-9bf8-4a53cb9e0739.
Timetable with sessions and material will be continuously updated towards the workshop.
28th January
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 08:30 | Registration | ||
| 09:15 | Welcome and introduction | Slides | |
| 09:45 | Deployment and platform options | Slides | |
| 11:00 | Get a basic Galaxy server up and running | Slides | |
| 12:00 | 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) |
| 15:30 | Defining and importing genomes, Data Managers | Slides, Exercise | |
| 17:00 | Extending your installation: FTP, SMTP, and more | Slides, Exercise | |
| 16:00 | Close Day 1 |
29th January
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | ||
| 09:15 | Users, Groups, and Quotas | Slides | |
| 11:00 | Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools | Slides (Shed), Slides (Tools), Slides (Dependencies) | |
| 13:15 | Updating tools and supporting multiple versions of tools | Exercise | |
| 14:30 | Improving the web serving experience with uWSGI | Slides, Exercise | |
| 15:45 | Controlling Galaxy with systemd and supervisor | Slides, Exercise | |
| 16:45 | Using and configuring external authentication services | Slides, PAM Auth Exercise, Upstream Auth Exercise | |
| 17:00 | Close Day 2 |
30th January
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | ||
| 09:15 | Exploring the Galaxy job configuration file | Slides | (N) |
| 09:50 | Connecting Galaxy to a compute cluster | Slides, Exercise | |
| 11:00 | Connecting Galaxy to a compute cluster (continued) | ||
| 13:30 | Configuration management choices: Introduction to Ansible | Slides | |
| 14:00 | Using Ansible to deploy Galaxy | Exercise 1, Exercise 2 | |
| 15:45 | Using Ansible to deploy Galaxy (continued) | ||
| 16:45 | Using heterogeneous compute resources | Slides, Exercise | |
| 17:00 | Close day 3 |
31th January
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | ||
| 09:15 | Storage management and using heterogeneous storage services | Slides, Exercise | |
| 11:00 | Containerize all the things: Galaxy in Docker and Docker in Galaxy | Docker Slides, Conda Slides, Galaxy Docker tool example | |
| 13:15 | Running Jupyter in Galaxy with Galaxy Interactive Environments | Exercise | |
| 15:45 | Using public and private cloud compute resources | Slides | |
| 16:30 | Server monitoring and maintenance: Admin UI, Log files, Direct database queries, command line & scripts, what to backup and how | Slides, Exercise 1, Exercise 2 | (B,M) |
| 17:00 | Wrap up and close |
2nd February
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | ||
| 10:15 | Upgrading to a new Galaxy release | Slides | (N) |
| 11.00 | What's new in Galaxy 18.01? | Slides | (N) |
| 13:30 | When things go wrong: Galaxy Server Troubleshooting | Slides | |
| 17:00 | Wrap up and close |
- (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
- Simon Gladman - Melbourne Bioinformatics, University of Melbourne, Australia
- Helena Rasche - ELIXIR Galaxy WG, Elixir Germany, de.NBI, University of Freiburg, Germany