Starting with Galaxy

Keywords: Galaxy, Microbial Genomics Virtual Lab

Background

Galaxy is a web-based analysis and workflow platform designed for biologists to analyse their own data. It can be used to run a variety of bioinformatics tools. The selection of bioinformatics tools installed on the Galaxy instance we are using today caters for the analysis of bacterial genomics data sets.

Galaxy is an open, web-based platform. Details about the project can be found here.

The Galaxy interface is separated into three parts. The Tools list on the left, the Viewing panel in the middle and the analysis and data History on the right.

galaxy overview screenshot

Register

Open a new tab or window on your web browser. Use Firefox or Chrome - please don’t use Internet Explorer or Safari.

In the address bar, type in the address of your galaxy server.

Galaxy URL

Click on User button on the right.

Register or Login screenshot

  • Select: User → Register
  • Enter your email, choose a password, and choose a user name.
  • Click Submit

  • Login, and refresh the page.

Import a history

Copy this link:

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Galaxy_history_input_files.tar.gz

  • Click on the History cog cog icon
  • Select Import from File

history options

  • In the box called Archived History URL, paste in the link address to the Galaxy history (that you copied above).
  • Click Submit
  • Wait a few seconds.
  • Click on the view all histories button histories icon
  • See if the Galaxy history has been imported: it will be called imported from archive: Data
  • Above that pane, click on the Switch to button.
  • Then click Done (in the top left corner).
  • You should now have a list of five files in your current history. We will use these for the Genomics Workshop; or see below for additional files.

files in galaxy history

Other ways to import data into Galaxy

  • Upload a file from your computer
  • Import a shared history
  • See the next section for more detailed information.