Creating a new tutorial - Creating Interactive Galaxy Tours

Overview

question Questions
  • What is a Interactive Galaxy Tour?
  • How can we create an Interactive Tour?
objectives Objectives
  • Creating a Galaxy tour from scratch
  • Deploying and running a tour

time Time estimation: 15 minutes

Introduction

Galaxy is a great solution to train the bioinformatics concepts:

  • numerous bioinformatics tools are available (almost 5,000 in the ToolShed)
  • it can be used by people without any computer science skills
  • it trains to use technology, outlining available resources and efforts that have made them accessible to researchers
  • it is scalable

In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as most of the time in Galaxy.

We take inspiration from Software Carpentry. We collected everything on a GitHub repository: https://github.com/galaxyproject/training-material . We decided a structure based on tutorials with hands-on, fitting both for online self-training but also for workshops, grouped in topics. Each tutorial follows the same structure and comes with a technical support to be able to run.

In this tutorial, you will understand how to design and develop a new tutorial fitting in this training material repository. As doing helps to understand, we will develop a small tutorial to explain BLAST with the full infrastructure to be able to run this tutorial anywhere.

Agenda

In this tutorial, we will deal with:

  1. A Galaxy Interactive Tour
  2. Creating a Galaxy Interactive Tour

A Galaxy Interactive Tour

A Galaxy Interactive Tour is a way to go through an entire analysis, step by step inside Galaxy in an interactive and explorative way. It is a great pedagogic way to run the tutorial directly inside Galaxy.

Demonstration of an Interactive Tour
Figure 1: Demonstration of an Interactive Tour

A tour is a YAML file like:

id: galaxy_ui
name: Galaxy UI
description: A gentle introduction to the Galaxy User Interface
title_default: "Welcome to Galaxy"

steps:
    - title: "Welcome to Galaxy"
      content: "This short tour will guide you through Galaxy's user interface.<br>
                You can navigate with your arrow keys and leave the tour at any time point
                with 'Escape' or the 'End tour' button."
      backdrop: true

    - title: "Upload your data"
      element: ".upload-button"
      intro: "Galaxy supports many ways to get in your data.<br>
              Use this button to upload your data."
      position: "right"
      postclick:
        - ".upload-button"
  • at the top some metadata related to the Tour:
    • id: ID of the tour
    • name: name of the tour
    • description: a short description of the tour
    • title_default: a title
  • several steps corresponding to the different boxes

    Each step is beginning with a dash - and with possible arguments

    Argument Description
    title Header of each step-container
    content Text that is shown to the user
    element JQuery Selector of the element you want to describe / click
    placement Placement of the text box relative to the selected element
    preclick or postclick Elements that receive a click() event before (preclick) or after (postclick) the step is shown
    textinsert Text to insert if element is a text box (e.g. tool search or upload)
    backdrop true/false: Show a dark backdrop behind the popover and its element, highlighting the current step

    Full reference of the properties

The YAML file of a tour can be integrated in a Galaxy instance by placing the YAML file in the config/plugins/tours directory of the Galaxy code and restarting the Galaxy instance

Creating a Galaxy Interactive Tour

A Web browser plugin is available to help the creation and the test (on the fly) of an interactive tour.

Galaxy Tour Builder by TailorDev

hands_on Hands-on: Install and start the plugin

  1. Install the plugin using the app store of your web-browser:
  2. Load the webpage of any Galaxy instance
  3. Start the plugin by clicking on the icon with Galaxy icon close to the address bar

We can now create easily a Galaxy Interactive Tour and test it on the fly.

hands_on Hands-on: Create a Galaxy Interactive Tour

  1. Create a Galaxy Interactive Tour for “BLAST” tutorial
  2. Test it with the plugin
  3. Copy the YAML content and add it to a file
  4. Add the file to the tours directory of the tutorial
  5. Test it on a local Galaxy instance

Conclusion

keypoints Key points

  • The Interactive Tours are a good training object for self-learning at its own speed
  • It is now easy to create an Interactive Tour and test it

congratulations Congratulations on successfully completing this tutorial!

Developing GTN training material

This tutorial is part of a series to develop GTN training material, feel free to also look at:
  1. Overview of the Galaxy Training Material
  2. Contributing with GitHub via command-line
  3. Contributing with GitHub via its interface
  4. Creating a new tutorial
  5. Creating a new tutorial - Creating Interactive Galaxy Tours
  6. Creating a new tutorial - Defining the technical infrastructure
  7. Creating a new tutorial - Slides
  8. Creating a new tutorial - Writing content in Markdown
  9. Generating PDF artefacts of the website
  10. Including a new topic
  11. Running the Galaxy Training material website locally