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
time Time estimation: 15 minutesSupporting Materials
last_modification Last modification: Jun 19, 2019
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.
In this tutorial, we will deal with:
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
Header of each step-container
Text that is shown to the user
JQuery Selector of the element you want to describe / click
Placement of the text box relative to the selected element
Elements that receive a click() event before (
preclick) or after (
postclick) the step is shown
Text to insert if element is a text box (e.g. tool search or upload)
true/false: Show a dark backdrop behind the popover and its element, highlighting the current step
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.
hands_on Hands-on: Install and start the plugin
We can now create easily a Galaxy Interactive Tour and test it on the fly.
hands_on Hands-on: Create a Galaxy Interactive Tour
- Create a Galaxy Interactive Tour for “BLAST” tutorial
- Test it with the plugin
- Copy the YAML content and add it to a file
- Add the file to the
toursdirectory of the tutorial
- Test it on a local Galaxy instance
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 materialThis tutorial is part of a series to develop GTN training material, feel free to also look at:
- Overview of the Galaxy Training Material
- Contributing with GitHub via command-line
- Contributing with GitHub via its interface
- Creating a new tutorial
- Creating a new tutorial - Creating Interactive Galaxy Tours
- Creating a new tutorial - Defining the technical infrastructure
- Creating a new tutorial - Slides
- Creating a new tutorial - Writing content in Markdown
- Generating PDF artefacts of the website
- Including a new topic
- Running the Galaxy Training material website locally
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