University of Utah
Salt Lake City, Utah
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 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.
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)
- Galaxy Tool Shed and Tool Installation
- Tool Shed intro
- Tool Installation
- Tool Management
- Advanced Tool Management
- Importing and defining reference genomes
- Extending the installation
- Users, groups, and quotas
Basics of Tool Definition & Planemo
- Upgrading Release
- Basic Troubleshooting
- Introduction to Galaxy Architecture
See the event GitHub page for details and resource links.
The Basics Session starts at 9:30am on Monday and Tuesday morning. Checkin and coffee opens at 9:15am. The sessions break for lunch and dinner (as well as morning and afternoon breaks). They wrap up both nights around 8:30pm.
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 .