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."
Salt Lake City - 7th to 11th November 2016
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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
- (D)an Blankenberg - Galaxy Project, BMB, Penn State University, USA
- (M)artin Čech - Galaxy Project, BMB, Penn State University, USA
- Dave (C)lements - Galaxy Project, Department of Biology, Johns Hopkins University, USA
7th November - Salt Lake City Library - Conference Room Level 4
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:15 | Check-in | ||
| 09:30 | Welcome and Introduction | Slides | All |
| 09:45 | Deployment and Platform Options | Slides | (N) |
| 10:15 | Get a Basic Galaxy Server Up and Running | Slides | (N + M) |
| 11:00 | Morning Break | ||
| 11:20 | Database choices and configuration. Introduction to PostgreSQL | Slides, Exercise | (N + M) |
| 12:20 | Lunch, catered | ||
| 13:20 | Web server choices and configuration. Introduction to Apache and NGINX. | Slides, Exercise 1, Exercise 2 | (N) |
| 14:20 | Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools | Slides (Shed), Slides (Tools), Slides (Dependencies), Exercise | (M) |
| 15:30 | Afternoon Break | ||
| 15:50 | Defining and importing genomes, Data Managers | Slides, Exercise | (S) |
| 17:40 | Dinner, on your own | ||
| 19:00 | Discussion, troubleshooting, ad hoc support | All | |
| 20:30 | Close Day 1 | All |
8th November - Salt Lake City Library - Conference Room Level 4
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:15 | Check-in | ||
| 09:30 | Welcome and Questions | All | |
| 09:45 | Extending your installation: FTP, SMTP, and more | Slides | (D) |
| 11:00 | Morning Break | ||
| 11:20 | Users, Groups, and Quotas | Slides | (D) |
| 12:20 | Lunch, catered | ||
| 13:20 | Anatomy of a Tool Definition, Planemo, Publishing | Slides | (S + M) |
| 14:50 | Updating tools and supporting multiple versions of tools | Exercise | (S + M) |
| 15:20 | Afternoon Break | ||
| 15:40 | Upgrading to a new Galaxy release | Slides | (N + M) |
| 16:50 | When things go wrong: Basic Galaxy server troubleshooting | Slides | (N + M) |
| 17:40 | Dinner, catered | ||
| 19:00 | Introduction to Galaxy Architecture (Joint session with the Advanced Topics session) | Slides | All |
| 20:20 | Wrap up and close | All |
9th November - Commander's house - North & South Parlor and Sun Room
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 08:30 | Check-in | ||
| 09:00 | Welcome and Introduction/Questions | All | |
| 09:20 | Configuration management choices: Introduction to Ansible | Slides, Exercise | (S) |
| 09:50 | Using Ansible to deploy Galaxy I | Exercise | (S) |
| 10:30 | Morning Break | ||
| 10:50 | Using Ansible to deploy Galaxy II | uWSGI slides | (S + N) |
| 12:20 | Lunch, catered | ||
| 13:20 | Server monitoring and maintenance: Admin UI, Log files, Direct database queries, Command line & scripts, What to backup and how | Slides | (S + N) |
| 15:20 | Afternoon Break | ||
| 15:40 | Controlling Galaxy with systemd and supervisor | Slides, Exercise | (N) |
| 16:10 | Advanced tool definition, tool failures, tool debugging | Slides | (M) |
| 17:40 | Dinner, on your own | ||
| 19:00 | Discussion, troubleshooting, ad hoc support | All | |
| 20:30 | Close day 1 | All |
10th November - Commander's house - North & South Parlor and Sun Room
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 08:30 | Check-in | ||
| 09:00 | Welcome and Introduction/Questions | All | |
| 09:20 | Using and configuring external authentication services | Slides, Exercise | (M + N) |
| 10:30 | Morning Break | ||
| 10:50 | Connecting Galaxy to a compute cluster I | Slides, Exercise 1, Exercise 2 | (N) |
| 12:20 | Lunch, on your own | ||
| 13:20 | Connecting Galaxy to a compute cluster II | (N) | |
| 15:20 | Afternoon Break | ||
| 15:40 | Using Heterogeneous compute resources | Slides, Exercise | (N) |
| 17:40 | Dinner, on your own | ||
| 19:00 | Using public and private cloud compute resources | Slides | (S) |
| 20:30 | Close day 2 | All |
11th November - Commander's house - North & South Parlor and Sun Room
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 08:30 | Check-in | ||
| 09:00 | Welcome and Introduction/Questions | All | |
| 09:20 | Storage management and using heterogeneous storage services | Slides, Exercise | (N + M) |
| 10:30 | Morning Break | ||
| 10:50 | Complex Galaxy servers examples: usegalaxy.org, GVL | Slides (usegalaxy.org), Slides (GVL) | (N + S) |
| 12:20 | Lunch, on your own | ||
| 13:20 | When things go REALLY wrong: Advanced Galaxy server troubleshooting | Slides | (N) |
| 15:20 | Afternoon Break | ||
| 15:50 | Participant selected topics | Interactive Environments: Jupyter | All |
| 17:30 | Dinner, catered | ||
| 18:50 | Discussion and open questions | All | |
| 20:30 | Wrap up and close | All |