Customizing the look of Galaxy (Manual)

Author(s) orcid logoLaila Los avatar Laila Los
Editor(s) orcid logoHelena Rasche avatar Helena Rasche
Creative Commons License: CC-BY Questions:
  • How do I change Galaxy’s front page?

  • How do I set a custom brand text?

  • How can I configure theming?

  • Set a brand text for your Galaxy instance

  • Add a custom welcome page to Galaxy

  • Activate and customize themes

Time estimation: 45 minutes
Supporting Materials:
Published: Apr 16, 2023
Last modification: Apr 15, 2023
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL:
version Revision: 5

Customizing your Galaxy instance makes it more recognizable at a glance, and can help communicate its purpose to its users. This tutorial will teach you three basic customizations you can make to Galaxy:

  • Setting a brand text
  • Adding a custom welcome page
  • Customizing the masthead using themes

For this tutorial we will be setting up a fictional instance called “Galaxy Mars”. Feel free to use the included material in the hands-on sections, or provide your own.

  1. Custom Branding
  2. Custom Welcome Page
  3. Custom Masthead Theme

Custom Branding

The brand text in Galaxy refers to the text you can see in the masthead of some Galaxy instances. This text will appear in the masthead, as well as the sites title. It is an easy way to set your instance apart, and make it more identifiable.

screenshot of the start page of Galaxy Europe. Open image in new tab

Figure 1: Galaxy Europe uses the brand text \"Europe\"
Hands-on: Customising the Branding
  1. Open your galaxy config file config/galaxy.yml and add the following option under galaxy:

    brand: Mars
    logo_src: ""
  2. Start your galaxy server using sh

  3. Navigate to https://localhost:8080

    screenshot of fictional "Galaxy Mars" start page, with the brand text set to "Mars". Open image in new tab

    Figure 2: Your Galaxy start page should now look like this

Custom Welcome Page

The welcome page is an html document embedded in Galaxy’s start page. It is what users see when first navigating to your instance. This page can be used to communicate what your instance is about, and share news and updates with your users.

Hands-on: Creating a custom welcome page
  1. (optional) Set the location of your welcome page in galaxy.yml

    Under galaxy: add the following option:

    welcome_url: /static/your-welcome-page.html

    Not setting this will cause the url to default to /static/welcome.html

  2. Open /static/welcome.html, or create a new html file at the location set in Step 0

    It is advisable to keep a copy of the default welcome.html, as it can serve as a useful reference.

  3. Add some Content

    Let’s add a title and some text to our welcome page:

    <!DOCTYPE html>
    <html lang="en">
            <meta charset="utf-8">
            <h1>Welcome to the Galaxy Mars instance!</h1>
            <p>The only Galaxy instance on mars.</p>

    This works the same as any other html page. You can add styles in the head, or import some scripts.

    Make sure your welcome page has exactly one h1 element, which describes the page. This will act as the heading for your start-page, which can help assistive technologies.

A lot of the UseGalaxy.* instances choose to use their welcome.html to display an IFrame to a different site, e.g. the site, or a sub-site thereof.

This makes it easier for non-administrators to keep the homepage’s contents up to date. By embedding (for example) a Wordpress blog in the center, non-technical contributors can still publish articles and announcements without having to re-deploy Galaxy every time.

As in our example welcome.html, we’ve loaded the default Galaxy CSS to keep it consistent with the surrounding material. If you wish to load a different CSS file, or set a different font for the main panel, you can easily do that by adding whatever CSS you like.

Custom Masthead Theme

Galaxy’s theming system allows you to easily change the color of your Masthead, to give your instance an even more distinct look. You can even offer several options, to allow users to switch to the default if they prefer it, or another look all together.

Hands-on: Configuring Themes
  1. (optional) Set the location of the themes configuration galaxy.yml

    Under galaxy: add the following option:

    themes_config_file: your-themes-file.yml

    This location is relative to the config directory. If unset, the default file themes_conf.yml will be used, if present.

  2. Create your themes config file.

    Open themes_conf.yml.sample, and copy its contents into a new file, either called themes_conf.yml, or the custom path you set in step 0. Do not copy the conf file and remove the ending, as this file is a symbolic link. Copying it copies a reference to the source file, not its contents.

  3. Understanding Themes

    The themes file can contain several themes. Each theme is identified by its id, eg blue, and followed by a set of rules, which style the client. The first theme in your theme file will be used as the default theme, which users see when visiting your instance, and which users who haven’t logged in will see.

    At the time of writing, themes only support styling the masthead, but this is subject to change. The first example theme should contain all available values you can change.

  4. Creating our own Theme

    Let’s create a theme more fitting for our Mars instance.

    Create a new theme, by adding mars: to the top of the themes config file. Now add masthead: underneath, and then color:. Set color to "#e03e1d", a nice deep martian red.

    Your theme file should now begin with:

        color: "#e03e1d"

    Restart your instance, and look at the masthead. It should be colored red.

  5. You can also try logging in, and changing your theme under Preferences