8.2 Getting Started
8.2.1 Set Up
In the next few steps, you will walk through how to get set up to use Galaxy on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment.
Use a web browser to go to the AnVIL website. In the browser type:
anvil.terra.bioTip At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other.
After logging in, click “View Workspaces”. Select the “Public” tab. In the top search bar type the activity workspace “SARS-CoV-2-Genome”. You can also go directly to the following link: https://anvil.terra.bio/#workspaces/gdscn-exercises/SARS-CoV-2-Genome.
Clone the workspace by clicking the teardrop button (
). And selecting “Clone”.
In the first box, give your Workspace clone a name by adding an underscore (“_”) and your name. For example, “SARS-CoV-2-Genome_Ava_Hoffman”. Next, select the Billing project provided by your instructor. Leave the bottom two boxes as-is and click “CLONE WORKSPACE”.
8.2.2 Starting Galaxy
Galaxy is a great tool for performing bioinformatics analysis without having to update software or worry too much about coding. In order to use Galaxy, we need to create a cloud environment. This is like quickly renting a few computers from Google as the engine to power our Galaxy analysis.
In your new Workspace, click on the “NOTEBOOKS” tab. Next, click on “Create a Cloud Environment for Galaxy”. You should see a popup window on the right side of the screen. Click on “NEXT” and “CREATE” to keep all settings as-is. This will take 8-10 minutes. When it is done, click “LAUNCH GALAXY”.
You can also follow along with the first ~2 minutes of this video to start Galaxy on AnVIL.
8.2.3 Navigating Galaxy
Notice the three main sections.
Tools - These are all of the bioinformatics tool packages available for you to use.
The Main Dashboard - This contains flash messages and posts when you first open Galaxy, but when we are using data this is the main interface area.
History - When you start a project you will be able to see all of the documents in the project in the history. Now be aware, this can become very busy. Also the naming that Galaxy uses is not very intuitive, so you must make sure that you label your files with something that makes sense to you.
On the welcome page, there are links to tutorials. You may try these out on your own. If you want to try a new analysis this is a good place to start.