bioinformatics.ca logo

  • CBW Bookdown Guide
  • I Introduction
  • 1 CBW’s Bookdown Documentation
  • 2 How Bookdown Works: A Primer
  • II Cheat Sheets
  • 3 Editing Your Workshop
  • 4 Handy Shortcuts
    • 4.1 Getting to your folder in the terminal
    • 4.2 Opening your folder from the terminal
    • 4.3 Commenting and uncommenting in RStudio
  • 5 FAQs
    • 5.1 Why aren’t my changes appearing on the website?
    • 5.2 What are the unusual symbols I’m seeing?
  • III Setup and Installations
  • 6 Installations
  • 7 Local Setup and SSH
    • 7.1 SSH Connection
      • 7.1.1 Generate an SSH key
      • 7.1.2 Add your SSH key to the ssh-agent
      • 7.1.3 Add your SSH key to your GitHub account
    • 7.2 GitHub Folder
      • 7.2.1 Create your folder
      • 7.2.2 Clone the GitHub homepage
      • 7.2.3 Clone the travel logistics repo
  • IV Set Up Workshop Site
  • 8 Create your repo
    • 8.1 Option 1: New repo
    • 8.2 Option 2: Duplicate existing repo
  • 9 Configure your repo
    • 9.1 A note on repos vs websites
  • 10 Deploy your site
    • 10.1 Check your deploy and see your website!
    • A very specific build and deployment warning
  • 11 Faculty team setup
  • 12 Clone to your computer
    • 12.1 Oops, I Git Cloned the Wrong Repository!
  • 13 Finishing touches
  • 14 Link to homepage
    • 14.1 Get your code
    • 14.2 Add to GitHub homepage
    • 14.3 Add to GitHub sitemap
    • 14.4 Update the website
  • 15 Logistics page
    • 15.1 Create your logistics page
  • 16 What’s next?
    • 16.1 Homepage
      • 16.1.1 Pre-work
      • 16.1.2 Schedule
      • 16.1.3 Class photo
    • 16.2 Faculty pages
    • 16.3 Computing
    • 16.4 Modules
      • 16.4.1 Embedding slides
      • 16.4.2 Embedding YouTube videos
      • 16.4.3 Adding lab material
    • 16.5 Bioschemas
    • 16.6 What if I need to add a new file or change the existing file structure?
  • V Formatting
  • 17 Markdown
    • 17.1 Formatting your content
      • 17.1.1 Option: Visual R Markdown
    • 17.2 Chapters and subheaders
      • 17.2.1 Sub-subheader
      • An unnumbered subheader
    • 17.3 Parts
    • 17.4 Text Formatting
      • Bold
      • Italics
      • Subscript
      • Superscript
      • Footnotes
      • Horizontal Line
      • Blockquote
      • Unordered List
      • Ordered List
      • Code
    • 17.5 Links
      • External webpages
      • Other sections within your workshop website
    • 17.6 Embedding
      • Images
      • PDFs
      • YouTube Videos
    • 17.7 Citations
    • 17.8 Equations
    • 17.9 Theorems and Proofs
    • 17.10 Using HTML
  • 18 Callouts
    • 18.1 Basic Syntax
    • 18.2 Attribute Reference
    • 18.3 Default Icons
    • 18.4 Examples
      • 18.4.1 Example 1: Informational Note
      • 18.4.2 Example 2: Collapsible “Plain” Answer Box
      • 18.4.3 Example 3: Important Red Warning
      • 18.4.4 Example 4: Comprehensive Dropdown
    • 18.5 Nesting Callouts
      • 18.5.1 Example of a Nested Callout
  • 19 Code
    • 19.1 Rendering Code
    • 19.2 Syntax highlighting
    • 19.3 Running code
    • 19.4 Code Chunk Options
    • 19.5 Code Chunks for Code-Generated Figures and Tables
  • VI Reference Material
  • 20 Command line crash course
    • 20.1 Terminal, Command Prompt and Windows PowerShell
    • 20.2 Common Commands (for us)
  • 21 Bookdown crash course
    • 21.1 How Bookdown works
    • 21.2 File setup
      • _output.yml & _bookdown.yml
      • Organizing the TOC: .Rmd files
      • Folders
    • 21.3 Working with your Bookdown project in RStudio
      • 21.3.1 Opening your Bookdown project
    • 21.4 Explaining RStudio
    • 21.5 Build the Book
      • 21.5.1 Other Ways to Build Your Book
      • 21.5.2 Knit Your Book
      • 21.5.3 Knit VS Build
      • 21.5.4 Preview Your Book
    • 21.6 Pushing to GitHub
  • Appendices
  • A Appendix A: developers’ guide
    • A.1 GitHub Repo
    • A.2 Diagram Links
      • A.2.1 How to Publish a Google Drawing
  • B Appendix B: homepage guide
    • B.1 Project Structure
    • B.2 How to Update Content
      • B.2.1 Add Your Image
      • B.2.2 Edit workshops.json
      • B.2.3 Example Entry:
    • B.3 Local Development & Validation
      • B.3.1 Live Validation in VS Code (Recommended)
      • B.3.2 Manual Validation via Command Line
    • B.4 Deployment
    • B.5 Common Debugging Steps
      • B.5.1 Symptom: The page is blank or workshops are not displaying.
      • B.5.2 Symptom: My recent changes are not appearing on the live site.
      • B.5.3 Symptom: A workshop card is showing a broken image.
  • C References
  • Sponsors

    Canadian Institutes of Health Research logo. Genome Canada logo. Ontario Genomics logo.

    Ontario Institute for Cancer Research logo.

CBW Bookdown Guide

14 Link to homepage

Note

You can find more info on the Github homepage setup in Appendix B.

For the best experience, we strongly recommend setting up the local validation system described here.

14.1 Get your code

  1. Use the below widget to generate your metadata entries for the website.

       Metadata generator

14.2 Add to GitHub homepage

  1. Navigate to your bioinformaticsdotca.github.io repo in your CBWGithub folder.

  2. Run git pull. You can do this in Terminal/PowerShell, or if you prefer, you can use an integrated Git system in your code editor.

  3. Open the img/ folder and look to see if your workshop icon is present.

  • If it is, make note of the filename.
  • If not, add your icon to that folder. The naming convention is CODE_icon.[extension] (e.g. INR_icon.png, GPO_icon.jpg)
  1. Open the workshops.json file and paste the first output from the widget below the first square bracket.

14.3 Add to GitHub sitemap

  1. Open the sitemap.xml file and paste the second output below the ``<urlset …>``` line at the top.

14.4 Update the website

  1. Git add, commit, and push the file. Code for use on the command line is below.

    git add workshops.json sitemap.xml
    git commit -m "YOUR MESSAGE HERE"
    git push
       Why don’t I need to run a Build step like I did for my Bookdown workshop website?

    The logistics pages and homepage use a different site generator than your workshop pages do. For updates to appear on the logistics and home pages, all you need to do is save your changes and push them to GitHub. The sites will automatically update.

  2. Go to the actions page and confirm that your update deploys successfully. This page has built-in validation: if your data does not match the expected format, deployment will fail.

       Why is the homepage displaying a picture of a laptop instead of my workshop icon?

    This is a generic 404 image - the website cannot find your icon. Double-check the filename and filepath in the workshops.json file, and double-check that your icon is named correctly.