Oslo, 8th to 12th January 2018
jump to Monday | Tuesday | Wednesday | Thursday | Friday
Built slides have an index.
Questions, topic nominations, lightning talk self-nominations, other info (Google Doc)
IMPORTANT! Workshop Evaluation form (please help us to be better)
- (B)jörn Grüning - ELIXIR Galaxy WG, Elixir Germany, de.NBI, University of Freiburg, Germany
- (M)arius van den Beek - ELIXIR Galaxy WG, Institute Curie, Paris, France
- (N)icola Soranzo - ELIXIR Galaxy WG, Earlham Institute, UK
- (E)nis Afgan - Galaxy Project, Johns Hopkins University, USA
- (A)bdulrahman Azab - ELIXIR Galaxy WG, PRACE, NeIC, USIT, University of Oslo, Norway
Building: Ole Johan Dahls hus, University of Oslo
Room: Seminar room Prolog (Room number: 2465, 2nd floor)
Timetable with sessions and material will be continously updated towards the workshop.
2 cores, 4 GiB memory, and 20 GiB disk
8th January - Location
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 08:30 | Registration | ||
| 09:15 | Welcome and introduction | Slides | All |
| 09:45 | Deployment and platform options | Slides | (B) |
| 10:45 | Morning break | ||
| 11:00 | Get a basic Galaxy server up and running | Slides | (A) |
| 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) |
| 12:30 | Lunch | ||
| 13:15 | Galaxy server optional necessities: PostgreSQL and nginx (continued) | (N) | |
| 15:15 | Afternoon break | ||
| 15:30 | Defining and importing genomes, Data Managers | Slides, Exercise | (E) |
| 17:00 | Extending your installation: FTP, SMTP, and more | Slides, Exercise | (A) |
| 18:00 | Close Day 1 | All |
9th January - Location
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09:15 | Users, Groups, and Quotas | Slides | (B) |
| 10:45 | Morning break | ||
| 11:00 | Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools | Slides (Shed), Slides (Tools), Slides (Dependencies) | (M) |
| 12:30 | Lunch | ||
| 13:15 | Updating tools and supporting multiple versions of tools | Exercise | (M) |
| 14:30 | Improving the web serving experience with uWSGI | Slides, Exercise | (B) |
| 15:30 | Afternoon break | ||
| 15:45 | Controlling Galaxy with systemd and supervisor | Slides, Exercise | (E) |
| 16:45 | Using and configuring external authentication services | Slides, PAM Auth Exercise, Upstream Auth Exercise | (N) |
| 18:00 | Close Day 2 | All |
Free common dinner at 7pm at Elias mat og sånt located downtown.
10th January - Location
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09:15 | Exploring the Galaxy job configuration file | Slides | (N) |
| 09:50 | Connecting Galaxy to a compute cluster | Slides, Exercise | (B) |
| 10:45 | Morning break | ||
| 11:00 | Connecting Galaxy to a compute cluster (continued) | (B) | |
| 12:30 | Lunch | ||
| 13:15 | Configuration management choices: Introduction to Ansible | Slides | (E) |
| 14:00 | Using Ansible to deploy Galaxy | Exercise 1, Exercise 2 | (E) |
| 15:30 | Afternoon break | ||
| 15:45 | Using Ansible to deploy Galaxy (continued) | (E) | |
| 16:45 | Using heterogeneous compute resources | Slides, Exercise | (M) |
| 18:00 | Close day 3 | All |
11th January - Location
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09:15 | Storage management and using heterogeneous storage services | Slides, Exercise | (E) |
| 10:45 | Morning break | ||
| 11:00 | Containerize all the things: Galaxy in Docker and Docker in Galaxy | Docker Slides, Conda Slides, Galaxy Docker tool example | (B) |
| 12:30 | Lunch | ||
| 13:15 | Running Jupyter in Galaxy with Galaxy Interactive Environments | Exercise | (B) |
| 15:30 | Afternoon break | ||
| 15:45 | Using public and private cloud compute resources | Slides | (E) |
| 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) |
| 18:00 | Wrap up and close | All |
12th January - Location
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Welcome and questions | All | |
| 09.15 | OPEN: Lightning talks | Trainees | |
| 10:15 | Upgrading to a new Galaxy release | Slides | (N) |
| 10:45 | Morning break | ||
| 11.00 | What's new in Galaxy 18.01? | Slides | (N) |
| 12:30 | Lunch | ||
| 13:15 | Trainees' feedback survey | Form | Trainees |
| 13:30 | When things go wrong: Galaxy Server Troubleshooting | Slides | (M) |
| 15:30 | Wrap up and close | All |