Running the GTN website online using GitPod

Author(s) orcid logoSaskia Hiltemann avatar Saskia Hiltemann
Reviewers Saskia Hiltemann avatar Helena Rasche avatar
Overview
Creative Commons License: CC-BY Questions:
  • How can I get a preview of the GTN website using GitPod?

Objectives:
  • Preview the GTN website online via GitPod

  • Make changes to the GTN website and preview those changes

Time estimation: 15 minutes
Supporting Materials:
Published: Jun 24, 2021
Last modification: Nov 8, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00066
rating Rating: 3.0 (1 recent ratings, 6 all time)
version Revision: 12

If you are working on your own training materials and want preview them online without installing anything on your computer, you can do this using GitPod!

Agenda

In this tutorial, you will learn how to run a local instance of the GTN website:

  1. Setting up Gitpod
  2. The GitPod Workspace
  3. Build and preview the GTN website
  4. Editing Training Materials on GitPod
  5. Saving your changes back to GitHub
  6. Closing your GitPod Workspace

Setting up Gitpod

Hands-on: Setting up GitPod
  1. Create a fork of the GTN GitHub repository

    If you already have a fork, fantastic! But a common issue is that the main branch gets outdated, or your fork was from before we renamed the master branch to main.

    • Start by browsing to your fork in GitHub
    • Check the default branch that is shown.
      • Does it say master? Then you need to update it, following the instructions below
      1. Go to your fork’s settings (Click on the gear icon called “Settings”)
      2. Find “Branches” on the left
      3. If it says master you can click on the ⇆ icon to switch branches.
      4. Select main (it may not be present).
      5. If it isn’t present, use the pencil icon to rename master to main.
      6. Now you can update it in the next step
    • Click the Sync Fork button on your fork to update it to the latest version

      Github with the top bar of a repository shown, including the button for 'Sync Fork'.

  2. Open your browser and navigate to gitpod.io/login
    • Note: don’t leave the /login part of the URL off, it will lead you to a different flavour of GitPod. We are using Gitpod classic
  3. Log in with GitHub GitPod sign-in menu with various options, including GitHub.
  4. Click on Configure your own repository under the Workspaces menu GitPod homepage.
  5. Under Select a repository choose your fork, e.g. https://github.com/shiltemann/training-material screenshot of new workspace menu.
  6. Click continue
    • This will create an enviroment where you can make changes to the GTN and preview them
    • Note: It can take quite some time to start up the first time (15-30 minutes)
    • We can make future starts a lot faster using prebuilds (see tip box below), you can configure this now while you wait

    progress indicator of GitPod first setup.

    Prebuilds can speed up the launch of your GitPod workspace after the first time. When this is enabled, starting a workspace will check if there is a previous build to reuse. This should bring startup times down to 3-5 minutes.

    Enable Prebuilds

    1. On the GitPod website, click on your name in the top left of the screen
    2. Select Repositories
    3. Add your fork as a repository
    4. On the left, click Prebuild settings
    5. Click the slider in front of Prebuilds are disabled to toggle the setting
    6. Set Branch Filter to Default Branch

    screenshot of prebuild setting of our repository.

    Run a prebuild now

    1. In GitPod, click on your name in the top left of the screen
    2. Select Prebuilds
    3. Click Run a Prebuild
    4. Select a Repository: your fork
    5. Click Run Prebuild
      • This will also take a bit of time to complete
      • In the future, it will automatically refresh this prebuild every 20 commits, so you only have to do this once

    Note: Prebuilds expire if you haven’t used them in 7 days, so if you have taken a longer break from GTN you might have to wait longer again the first time. But otherwise it should bring the launch time down to around 3-5 minutes.

  7. Once the setup is finished, you should see a page something like this: GitPod welcome screen.

    1. To make this even easier, you can install the GitPod browser extension
    2. Now it is just a single click to open any GitHub repository in GitPod screenshot of the button the GitPod browser extension adds to GitHub repository .

The GitPod Workspace

Let’s have a closer look at the GitPod workspace:

  • Left: Here you see all the files in the GTN repository
  • Top: This is the main window where you can view and edit files
  • Bottom: Terminal window. Here you can type commands (e.g. to build the website preview) and read output and error messages.

GitPod welcome screen.

Build and preview the GTN website

Before we start making any changes, let’s build the website and get a live preview.

Hands-on: Setting up GitPod
  1. In the terminal window (bottom), type the following command: make serve-gitpod

    output in the terminal after issuing the make serve-gitpod command.

  2. The first time you run this command, it will install some dependencies, so it may take a little bit of time (a few minutes)
    • Next times will be a lot faster! (~30 seconds)
  3. When the build process is finished, the terminal will show you a link, and a window should popup with a preview on the right.
    • You may have to click the “Try Again” button if the preview was generated before the site building completed

      gitpod with the GTN open in the right panel.

    • Click on the link in the terminal to see the GTN in full-screen: Server address: http://127.0.0.1:4000/training-material/

    output in the terminal after the build process has completed .

    screenshot of firefox permissions dialog which shows blocked windows and an allow menu. Some browsers block popups by default, you may need to allow GitPod to show popups in order to click links.

  4. This will take you to a preview of the GTN website
    • Note: It will take you the 404 page because GitPod doesn’t know the location of the GTN homepage, but from here you can just click the homepage button.

screenshot of gitpod's code editor with a tutorial open, and the GTN preview on the right.

Editing Training Materials on GitPod

Now that you have the GitPod environment working and we have a live preview up, let’s make some changes to the GTN materials and get an instant preview.

Scenario: You have spotted a typo in one of the tutorials, and would like to fix this and see the resulting GTN webpage.

Hands-on: Make and view changes
  1. In the preview of the GTN website, open the following tutorial:
    • Topic: “Introduction to Galaxy Analyses” topic
    • Tutorial: “A Short Introduction to Galaxy””
    • We will edit this tutorial and watch the live preview window for the effects
  2. On the file browser on the left, open the following file:

    topics/introduction/tutorials/galaxy-intro-short/tutorial.md
    

    You can use the key combination ctrl-p to launch the file search dialog and simply enter the text topics/introduction/tutorials/galaxy-intro-short/tutorial.md

  3. Change the title of the tutorial
    • From: “A Short Introduction to Galaxy”
    • To: “A Short and Cool Introduction to Galaxy”

    we changed the title of the tutorial in the text editor window.

    • You should immediately see a message in the terminal saying “regenerating”. GitPod has detected your changes and is rebuilding the website.

    the terminal shows a message stating the website is being regenerated.

  4. Move to the top right panel where the GTN is previewed and refresh the frame
    • galaxy-refresh Refresh button in front of the address bar of the preview panel
    • You can also open the preview in it’s own brower tab, using the galaxy_instance button at the top-right corner of the preview window. Then you can reload the page the regular way (e.g. F5 or ctrl + r or the reload button in the browser)
  5. You should see the change you made: The updated preview with our changed tutorial title.

In this way you can edit files in the text editor, and see the effects in the website preview.

Saving your changes back to GitHub

When you have finished your changes, it all looks good in the preview, you want to save your changes back to GitHub so that you can either continue later, or make a Pull Request to the GTN to contribute your changes.

Hands-on: Save changes
  1. Option 1: via the terminal
    • Hit ctrl+c if your preview was still running to stop it
    • Create a new branch, commit your changes, push changes:
    git checkout -b fix-title
    git commit -m "update tutorial title" topics/introduction/tutorials/galaxy-intro-short/tutorial.md
    git push origin fix-title
    
  2. Option 2: via the web interface
    • Create a new branch:
      • On the bottom-left, click on the branch logo (probably labelled “main”) button on the bottom of the page with the current branch.
      • Enter fix-title as the name for your new branch (at top of window)
      • Choose “+ Create new branch…” from the dropdown
    • Commit changes:
      • On the left menu, click on the “changed files” tab button on the left menu to show changed files.
      • Click on the “+” icon next to the file we edited to stage changes stage changes button.
      • Hit the checkmark icon at the top to commit the changes
      • Enter a commit message (top of window) - Publish changes
    • Click the cloud button at bottom left to publish your changes publish changes button.
  3. Your changes are now saved to your fork, and you can make a PR via the GitHub interface.
    • If you used option 1 and want to do that right away, you can click on the link in the terminal: link in the terminal to open a PR.

If this is your first time using GitPod, you may need to grant permissions to let GitPod push to your GitHub fork prompt to changes permissions. This will take you through a process to authorize GitPod, and set permissions permission settings for GitPod. If it doesn’t take you to GitPod’s permission page because your browser blocks popups, you can set them on this page.

Closing your GitPod Workspace

Everybody gets 50 hours per month for free on GitPod, so it is wise to close your GitPod workspace when you are finished with it, to conserve your quotum.

Hands-on: Shutting down your GitPod workspace
  1. Click on the menu button at the top left corner of the screen
    • Choose “Gitpod: Stop Workspace”

    stop workspace option in the main menu.