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Galaxy Administrators Course

Oslo, 8th to 12th January 2018

Event Logistics

jump to Monday | Tuesday | Wednesday | Thursday | Friday

Built slides have an index.

Galaxy Training material

Questions, topic nominations, lightning talk self-nominations, other info (Google Doc)

IMPORTANT! Workshop Evaluation form (please help us to be better)

Instructors

  • (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

Location

Building: Ole Johan Dahls hus, University of Oslo

Room: Seminar room Prolog (Room number: 2465, 2nd floor)

Timetable

Timetable with sessions and material will be continously updated towards the workshop.

Training VM instances (recommended specs)

2 cores, 4 GiB memory, and 20 GiB disk

Timetable

Monday

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

Tuesday

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.

Wednesday

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

Thursday

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

Friday

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

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Galaxy admin trainings for aspiring Skywalkers

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