Galaxy Admin Training: Basic Topics

Galaxy Project Admin Training November 7-11, 2016
University of Utah
Salt Lake City, Utah
United States

Register by October 16

Lodging released October 6

November 7-8, Salt Lake City Library

This two day introductory session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn and how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server as well.


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

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.


This two day workshop will cover the big picture, and installation, configuration, and customization basics. We'll present these topics by exploring several specific examples in detail. Participants will finish this workshop with a solid understanding of how to set up and customize a Galaxy instance running on a desktop or standalone server.

  • Deployment platform options
  • Installing a basic Galaxy server
  • Database choices and configuration (SQLite & PostgreSQL)
  • Web server choices and configuration (NGINX & Apache)
  • Identifying and installing well-defined tools from the Galaxy Tool Shed
  • Importing and defining reference genomes
  • Defining users, groups, and quotas
  • Basics of Tool Definition
  • Enabling extensions: FTP & SMTP
  • Introduction to Galaxy Architecture


This is a draft schedule and is a work in progress. Topic order and specific start and end times are likely to change.


Time Topic
9:15am Checkin and Coffee
9:30am Welcome and intro
10:00am Deployment and platform options
10:20am Get a basic Galaxy server up and running.
11:00am Break
11:20am Database choices and configuration. Introduction to PostgreSQL.
12:30pm Lunch Break
1:30pm Web server choices and configuration. Introduction to NGINX.
3:20pm Break
3:40pm Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools.
4:50pm Defining and importing genomes
5:40pm Dinner Break
7:00pm Defining and importing genomes, cont.; Data Managers
8:30pm Done


Time Topic
9:15am Coffee
9:30am Welcome, Questions
9:45am Extending your installation: Enabling FTP & SMTP
11:00am Break
11:20am Users, Groups, and Quotas
12:20pm Lunch Break
1:20pm Tool Definition Basics & Planemo
3:20pm Break
3:40pm Tool Definition Basics & Planemo, cont.
5:40pm Dinner Break
7:00pm Introduction to Galaxy Architecture (Joint session with the Advanced Topics session)
8:20pm Wrap-up
8:30pm Done

alt Lake City Main Public Library, the venue for the introduction workshop


The introductory training workshop will be held at the Salt Lake City Main Public Library. This stunning venue is located in downtown Salt Lake City at 210 East 400 South, and is a stop on the UTA TRAX Red Line and just 5 stops from conference housing. We'll be meeting in Conference Room 4 .

Questions? Contact [Galaxy Outreach](