tutorial.md

layout	title	questions	objectives	time_estimation	key_points	contributors
tutorial_hands_on	Creating a new tutorial - Creating Interactive Galaxy Tours	What is a Interactive Galaxy Tour? How can we create an Interactive Tour?	Creating a Galaxy tour from scratch Deploying and running a tour	15m	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	bebatut bgruening shiltemann

Introduction

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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. TOC {:toc}

{: .agenda}

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.

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

<script async src="//s.imgur.com/min/embed.js" charset="utf-8"></script>

{% icon hands_on %} Hands-on: Install and start the plugin

1. Install the plugin using the app store of your web-browser:

   • Chrome Web Store
   • Mozilla Add-ons (Firefox)
   • Opera add-ons

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 {: .hands_on}

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

{% icon 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 {: .hands_on}

Conclusion

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