Installing Galaxy for Bioinformatics on AWS


This guide is designed for those who already hold an AWS account and are subscribed to the Alces Flight Solo product. Brand new to all of this? Then check out our documentation on launching a HPC cluster on AWS.

A bit about Galaxy

The Galaxy application is described as an open-source, web-based platform for data intensive biomedical research. Galaxy has grown to be one of the most popular applications in life sciences and can be installed and configured in a few different ways. In this guide we’re going to look at one of the easier configurations, a single-user installation that runs as your user on the cluster login node. This could be extended to work with compute nodes by integrating with the cluster job scheduler or using Galaxy’s own job runner, Galaxy Pulsar.

Recommended AWS CloudFormation Selections for Compute Estate

When launching your Alces Flight Solo (Community Edition) cluster we’ve found some recommended settings and selections within the CloudFormation template outside of our standard configurations that will result in a successful installation. Never worked with CloudFormation before? Then check out our guide here.

Compute estate settings for optimal performance with the Galaxy Application

Installing Galaxy

We will be installing Galaxy Release 16.07 from GitHub. To do this from your terminal or shell enter:

Launching Galaxy from the web browser

From the Applications drop-down menu select Firefox Web Browser. Once open, type in the browser address:

But wait… there’s more…

In order to get the most out of your Galaxy installation you will need to change some of the default settings. First, let’s stop Galaxy running from the terminal inside of the graphical interface. To do so minimise your web browser and select the terminal. Press CTRL+C. You should get a stop message as follows:

Configuring Galaxy for optimal use

Enabling VPN Access

By default Galaxy enables local access only. To allow access from your VPN connected client we’ll modify the configuration to remove this restriction.

Promoting yourself to administrator

In order to gain administrative rights to Galaxy you first need to register yourself as a user. To do so select “Register” from the User menu the GUI and fill in the required information:

Installing Tools in Galaxy

Now that you’ve made yourself an administrator you can install tools into Galaxy. As an example, here’s how you would install a Fasta Manipulation tool:

To sum it up

This post provides a basic guide for installing Galaxy on Alces Flight Solo. In this installation you have:

  • Started your own personal HPC cluster
  • Installed and configured Galaxy
  • Connected to the web interface
  • Added tools into your Galaxy environment
  • Adding further storage volumes, and thinking about backup
  • Accessing the web interface from other locations
  • Installing additional instances as Galaxy worker nodes



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