The Galaxy Administrator Training Course – Melbourne will run for four days, Monday-Thursday, 6-9 February, starting right after the GAMe 2017 Conference. The course will take place at LAB-14, University of Melbourne, 700 Swanston St, Carlton.
Basic through advanced topics will be offered. Sessions will be intensive and hands-on, and taught by experienced instructors from the Genomics Virtual Lab and Galaxy Project teams. Participants will learn how to install, configure, customise, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community.
- Day 1:
Deployment and Platform Options
Get a basic Galaxy server up and running
Galaxy server optional necessities: PostgreSQL and NGINX (combined PostgreSQL and proxy sections, dropped Apache)
Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools
Defining and importing reference genomes, Data Managers
Extending your installation: FTP, SMTP, and more
- Day 2:
Users, Groups, and Quotas
Updating tools and supporting multiple versions of tools
Upgrading to a new Galaxy release
Improving the web serving experience with uWSGI
Server monitoring and maintenance: Admin UI, Log files, Direct database queries, Command line & scripts, What to backup and how
Using and configuring external authentication services
- Day 3:
Configuration management choices: Introduction to Ansible
Using Ansible to deploy Galaxy
Controlling Galaxy with systemd and supervisor
Connecting Galaxy to a compute cluster
Using Heterogeneous compute resources (Pulsar)
Using public and private cloud compute resources
- Day 4:
Storage management and using heterogeneous storage services
Containerize all the things: Galaxy in Docker and Docker in Galaxy
Running Jupyter in Galaxy with Galaxy Interactive Environments
Galaxy server troubleshooting
Advanced topics will use resources from the Nectar Cloud.
Please review the prerequisites carefully before registering. If you arrive without meeting the prerequisites then the workshop will be a frustrating experience.
Comfortable with the Unix/Linux command line
Most of the workshop will happen at the Linux command line. If you aren’t comfortable with this before you arrive, then you will be lost the entire time. How comfortable do you need to be? Here’s a sampling of commands and concepts that you should be comfortable with:
cd, mkdir, rmdir, ls tar, gzip cp, mv, rm, chmod, ln ~, .., ./, /tmp cat, tail, less man
Note: This is not an exhaustive list (or even a proper subset) of the commands that will be used in the workshop. They are included here to give you an idea of the depth of knowledge that is required.
Competent in a Unix/Linux text editor
Linux has several text editors available in it. You’ll need to be competent in at least one of them before the workshop starts. Organizers will make sure that these editors are available on the Linux images we use in the workshop:
- Nano: Simple and functional. Gets the job done.
- Emacs: Powerful and a wee bit scary.
- VIM: Powerful, efficient, and more than a wee bit scary.
Some experience with Linux Package Management
You don’t need to be an expert at Linux package management, but you do need to have some experience at installing and upgrading packages on a Linux system.
We’ll be using Ubuntu based images during the workshop, which means we’ll be using apt to do package management. Get to know it.
Hardware and Software
All participants should bring a wifi-enabled laptop with
- at least 4GB of memory (more is better)
- Software to access the command line of a Linux server.
- If you are running Linux or Mac OS, then you already have this.
- If you are running Windows than you’ll need to get something like putty installed before the workshop.
- A recent version of either the Chrome or Firefox web browser installed.
- Enis Afgan, Galaxy Project, Johns Hopkins University
- Nate Coraor, Galaxy Project, Penn State University
- Simon Gladman, VLSCI, University of Melbourne
- Björn Grüning, University of Freiburg
- Ross Lazarus, Galaxy Project, and formerly of BakerIDI
Praise for Galaxy Administrator Training
This workshop was presented by several of the same instructors, in November 2016, in Salt Lake City, Utah, United States. Feedback was very positive.