Based on the Minimal Mistakes Jekyll theme under and MIT license.

Website Configuration

Global settings

See full config. The following are the most important places where you need to make changes (see comments in these files also):

  • edit _config.yml to update site metadata
    • most important settings (site title, name, url) are highlighted at the top,
    • you can add Google Analytics tracking ID
  • edit _data/navigation.yml to add more tabs to the top navigation: title and url (relative to site url)
# main links in _data/navigation.yml
  - title: "Instructions"
    url: /
  - title: "Compute an E-value"
    url: /evalue/
  - title: "More resources"
    url: /resources/

Adding a new page

Open the site.Rproj file in RStudio IDE. Open Rmd files you’d like to edit. Click render. Jekyll will ignore Rmd, and will deploy html based on the md files.

Adding a new page under

  1. create folder path/dir
  2. add index.Rmd into the folder (see below for what goes into the header)
  3. Edit Rmd then render the md

This is the part that goes into the Rmd header of the file path/dir/index.Rmd:

title: Add your title here
layout: archive
    variant: gfm
    preserve_yaml: true

Keeping the layout and output is important, so that it will show up as expected after Jekyll renders the pages.

Note: if images are included as part of the Rmd, those will be placed relative to the index.Rmd file and need to be added to git.

See this cheat sheet for markdown formatting.

Adding new page for a Shiny app

Here is how you can add Shiny apps that are already deployed. (See Shiny app deployment below.)

Create new folder in the root, e.g. app and add app/ file with the following content: change the app url

layout: app

This will indicate to the Jekyll template to use the app layout (which puts the iframe around the app URL). The app_url is the link that will show up in the iframe.

If the website is served over https, the iframe needs to be https as well.

Website deployment

GitHub pages use Jekyll, so no additional steps are required. Commit changes and it is done. Make sure you go to the Settings tab of the repo and set GitHub pages deployment from the root folder of the master/main branch.

Custom domains

Set up a www subdomain: following this guide.

  1. Go to the Settings tab of the repo, scroll down to the GitHub Pages section
  2. Add to the Custom Domain field and click Save
  3. Go to your DNS settings on your provider’s page (see here)
  • In the first field, enter www or the required subdomain
  • In the dropdown menu, select CNAME
  • In the TTL field, enter 1H
  • In the data field, enter
  • Click Add

Editing the outer UI of the website

To edit the outer framework exclusive of the Shiny app iframe itself (e.g., the Resources tab), just edit and knit the relevant .Rmd file, commit as normal (with no special message), and push. Remember you need to knit the .Rmd file or else the changes will not be reflected in the .md file, which is what the website ultimately uses.

  • Changing font sizes: Edit per comments in assests/css/main.scss.
  • Changing fonts: Edit _sass/minimal-mistakes/_variables.scss (not tested).
  • Changing width of text on page (i.e., change whitespace on either side of text column): Edit per comments in _sass/minimal_mistakes/_archive.scss.

Note: We are using the “archive” layout (_sass/minimal_mistakes/_archive.scss), so if you want to change a parameter that is normally in _page.scss, you should change it in _archive.scss instead.

Deploying Shiny apps to Heroku

The shiny apps live inside the _shinyapps folder (Jekyll ignores directories that begin with underscore, thus we don’t need to worry about publishing the source code as part of the website).

The apps can be placed inside this folder, e.g.

  • _shinyapps/evalue
  • _shinyapps/app2

The structure inside the app folders can be identical:

  • _shinyapps/evalue/app/global.R: the global script
  • _shinyapps/evalue/app/ui.R: the UI
  • _shinyapps/evalue/app/server.R: the server function
  • _shinyapps/evalue/Dockerfile: see comments inside the file and prompts for where to edit.
  • _shinyapps/evalue/renv.lock: run renv::init() and/or renv::snapshot() to capture dependencies in the renv.lock file.

Edit the .R files as needed, add other scripts and data objects inside the app folder (this is copied into the Docker image).

Heroku deployment

This workflow works with public and private repositories.

  1. Log into Heroku, in the dashboard, click on ‘New’ then select ‘Create new App’. Give a name (e.g. shiny-example, if available, this will create the app at to the app and create the app.
  2. In your Heroku dashboard, go to your personal settings, find your API key, click on reveal and copy it, you’ll need it later.
  3. Go to the Settings tab of the GitHub repo, scroll down to Secrets and add the following new repository secrets:
  • HEROKU_EMAIL: your Heroku email that you use to log in
  • HEROKU_API_KEY: your Heroku api key, you can find it under your personal settings, click on reveal and copy
  1. Trigger the GitHub action by a new commit to the repo (see below).

See the .github/workflows/deploy.yml file for additional options (see also comments in the yaml file):

  • set the appdir variable to e.g. _shinyapps/evalue, this is the directory the script will use to find the Shiny files relative to the Dockerfile in the root of this directory
  • add the Heroku app name (shiny-example) that was set up in the Heroku dashboard previously
  • the job name must be unique in the yaml file to avoid parsing errors

The plan is to add multiple Shiny apps in the same GitHub repo, thus we need a mechanism that only deploys one app at a time. The solution is to make the GitHub action jobs conditional on certain words in the commit message. E.g. it only deploys if the message contains deploy evalue.

When you add a new app, the Heroku email and API key will remain the same. You will have to add a new job to the deploy.yml file, specify the trigger words, app directory, and app name.

Once the app is deployed, you can add a page and navigation entry for the new app as desired above.

Local development with jekyll

One-time steps to set up jekyll locally

Install jekyll (one time setup inside the directory): skip steps as appropriate, e.g. if you have Ruby installed etc (ruby -v should return Ruby version). See more about Ruby and Jekyll installation here.

This will install jekyll to evalue_website/vendor. Important: To avoid errors in bundle install, the entire file path to ruby (which will be in evalue_website/vendor) needs to not have spaces in the directory names. Change them to underscores before the installation.

# Install Command Line Tools
xcode-select --install

# Install Homebrew
/bin/bash -c "$(curl -fsSL"

# Install Ruby
brew install ruby

# Add the brew ruby path to your shell configuration:
PATH="`ruby -e 'puts Gem.user_dir'`/bin:$PATH"

# Install Jekyll
gem install --user-install bundler jekyll

# Install gems (dependencies) for the template
bundle install

When you edit your files and want to check locally how the site looks, first make sure you are in the top-level directory evalue_website (where the jekyll files live) and then use this:

bundle exec jekyll serve

This will build the site that you can check at in your browser. When you change the source it render the changes but you have to click refresh in the browser to see the changes. Stop the server with Ctrl+C in the command line.

Common error messages

  • If bundle exec jekyll serve fails with the error Configuration file: none, you are probably not in the top-level directory evalue_website.