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

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 shared history

For Galaxy-mel/Galaxy-qld users, import the following history:

  • In Galaxy, go to the top menu bar
  • Click on Shared Data

  • From the drop down menu, click on Histories

Drawing

  • From the list of Published Histories, click Genomics-workshop

published histories

  • In the top right, click on Import history

Drawing

  • This history will now be in your “Current history” - the right hand pane in Galaxy.
  • There should be six files. (The number in front of the file name is not important.)

Drawing

  • We will use these files for the Genomics Workshop. For additional ways to import histories, see below.

How to use Galaxy

  • Available tools are in the left hand panel. Find the tool you want or use the search bar at the top of the tools.

  • Click on the tool you want to use.

  • The tool interface will appear in the centre Galaxy panel. Check the settings.

  • Click Execute.

  • When the tool has finished, output file(s) will appear at the top of your “Current History” in the right hand panel.

  • Click on the eye icon next to a file to view it.

  • To access older histories, use the button at the top right of the History panel.

Alternative file import information

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.