2019 Galaxy Admin Training

The ins and outs of setting up your own production quality Galaxy server

Galaxy Admin Training will be offered January 28 through February 1 at Penn State University, where the Galaxy Project got started over ten years ago. The workshop is split into a 2 day introductory session and a 3 day advanced topics session. Participants can register for one or both sessions.

This workshop will cover basic and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. Participants will learn how to install, configure, customize, 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.

Galaxy is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life.

Schedule

The workshop is split into a 2 day introductory session and a 3 day advanced topics session.

Prerequisites

Please review the prerequisites carefully before registering. If you arrive without meeting the prerequisites then the workshop will be a frustrating experience.

Introduction Session

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.

Advanced Topics

Prerequisites include all of the Introduction Session prerequisites, plus familiarity with the topics presented in that session.

Laptop Requirements

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.

Instructors

We currently have five confirmed (and highly experienced!) instructors:

  • Martin Čech, software engineer for the Galaxy Project and frequent sys admin for usegalaxy.org.
  • Nate Coraor, lead sys admin for usegalaxy.org and a software engineer for the Galaxy Project
  • John Chilton, software engineer for the Galaxy Project working on both the front and back ends, with an emphasis on scalability.
  • Simon Gladman, administrator of Galaxy Australia (https://usegalaxy.org.au), University of Melbourne
  • Helena Rasche, administrator of Galaxy Europe (https://usegalaxy.eu) system administrator, University of Freiburg

Registration

Registration is open and is available on a first come, first served basis. Rates depend on your organization's non-profit status and when you register. The workshop is split into a 2 day introductory session and a 3 day advanced topics session. Participants can register for one or both sessions.

Space is limited and the 2016 and 2018 admin training workshops sold out. Register now.

Introduction to Galaxy Administration, 2 days

Early
by Oct 31
Advance
by Dec 31
Full
Non-profit / academic $80 $130 $190
Industry $120 $200 $320

Galaxy Administration Advanced Topics, 3 days

Early
by Oct 31
Advance
by Dec 31
Full
Non-profit / academic $120 $195 $285
Industry $180 $300 $480

Cancellations

  • Cancellations received before the early registration deadline (October 31) will receive a full refund.
  • Cancellations received after early registration closes, but before Advance registration closes (December 31) will receive a 50% refund.
  • Cancellations received after December 31 will not receive a refund.

Transportation

The easiest way to get to Penn State is the State College Airport (SCE). SCE is served by American, Delta, and United airlines and has multiple daily direct connections to Chicago, Detroit, Philadelphia, and Washington Dulles. SCE is less than a 15 minute ride from downtown State College.

Major international airports within a 4 hour drive of State College include Baltimore (BWI), Philadelphia (PHL), Pittsuburgh (PIT) - all ~ 3 hours; and Washington National (DCA) and Washington DULLES (IAD) both ~ 3.5 hours. Philadelphia and Pittsburgh have reasonable public transportation to State College (under 6 hours), but everywhere else you will definitely want to rent a car.

Lodging

There is no official lodging venue for this event. However, here are several places to consider:

  • Days Inn, in the State College city center. Close to restaurants, pubs and shopping, and a 14 minute walk to the workshop.
  • Hyatt Place, also in central State College, and a 16 minute walk.
  • Nittany Lion Inn, on the Penn State campus, and is an 18 minute walk to the workshop venue.
  • Atherton Hotel, in central State College and an 18 minute walk.

There are other less expensive, but more distant lodging options. State College has a public bus system (every route goes close to or through campus) and paid public parking is available on campus as well.