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Galaxy Administrators Course

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

Event Logisitics | Admin Training Home Page

jump to Monday | Tuesday | Wednesday | Thursday

Built slides have an index.

Instructors

  • (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:

spreadsheet

Timetable

Monday

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

Tuesday

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

Wednesday

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

Thursday

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
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