Galaxy admin trainings for aspiring Skywalkers
Clone or download
martenson Merge pull request #55 from ic4f/2019-pennstate
Multiple content updates (see comment)
Latest commit 03d2634 Nov 6, 2018

README.md

gat_pennstate_logo_wtext.png

Intro to Galaxy Administration @ Pennsylvania State University

Monday 1/28/2019 - Friday 2/1/2019

jump to Monday | Tuesday | Wednesday | Thursday | Friday

Built slides have an index.

Join the chat at https://gitter.im/dagobah-training/Lobby

Galaxy Training material

Location

TBA, State College, Pennsylvania, USA

Training VM instances

TODO fill this section

List of training instances is available in [TODO]. Please pick one instance and enter your name in the user column.

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

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

Basic Sessions

Monday

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

Tuesday

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

Advanced Sessions

Wednesday

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

Thursday

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

Friday

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

Instructors

  • (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