Girke Lab Site — Administration Guide

Internal documentation for site maintenance and content updates.
Live site: https://girke.bioinformatics.ucr.edu/
Repository: https://github.com/tgirke/tgirke.github.io

Table of Contents

Repository structure

tgirke.github.io/
├── _quarto.yml               # site config: navbar, theme, metadata
├── index.qmd                 # homepage
├── assets/
│   ├── logo.png              # navbar logo
│   ├── custom.scss           # light mode CSS overrides (UCR blue navbar)
│   └── custom-dark.scss      # dark mode CSS overrides
├── bio/index.qmd             # biography page
├── contact/index.qmd         # contact page
├── members/
│   ├── index.qmd             # members landing page
│   └── members.qmd           # members content
├── research/
│   └── publications/
│       └── publications.qmd  # publication list (reverse numbered)
├── software/index.qmd        # software packages
├── teaching/index.qmd        # teaching and courses
├── positions/index.qmd       # open positions
├── CNAME                     # custom domain — do not delete
├── README.md                 # public-facing repo description
└── ADMIN.md                  # this file

Local setup and preview

# Clone the repo
git clone git@github.com:tgirke/tgirke.github.io.git
cd tgirke.github.io

# Preview locally (ChromeOS/headless Linux — always use --no-browser)
quarto preview --no-browser
# Open http://localhost:5675/ in browser

# Render full site
quarto render

Requires Quarto installed locally: https://quarto.org/docs/get-started/

Daily workflow

git pull                        # always pull before editing
# ... make changes ...
quarto preview --no-browser     # check locally
git add -A
git commit -m "Description of changes"
git push origin main            # triggers automatic deploy via GitHub Actions

GitHub Actions and deployment

Every push to main triggers .github/workflows/publish.yml which renders the site and deploys to GitHub Pages automatically. Since this site has no R code chunks, the build is fast (~1-2 minutes).

Monitor builds at: https://github.com/tgirke/tgirke.github.io/actions

Important: The CNAME file at the repo root must never be deleted — it maps the custom domain girke.bioinformatics.ucr.edu to this repo. All other lab repos (GEN242 etc.) inherit this domain automatically.

Adding and updating content

Publications

The publications page uses a reverse-numbered CSS counter. The list is in research/publications/publications.qmd. Each entry uses 1. as the list marker — the CSS handles the countdown display.

When adding new publications, add them at the top of the list and update the counter in assets/custom.scss:

div.publications ol {
  counter-reset: pub-counter 109;  /* set to total publications + 1 */
}

Members

Edit members/members.qmd directly. Follow the existing card layout pattern for consistency.

Theme and styling

The site uses the slate Quarto theme (dark) with a UCR blue (#003da5) navbar in light mode.

assets/custom.scss — light mode overrides: - UCR blue navbar (#003da5) - Navbar text and icon colors - Publication list reverse counter - Code output box styling

assets/custom-dark.scss — dark mode overrides: - Dark navbar (#1a1a1a) - Sidebar and text colors - Code output box styling

To change the navbar color, update background-color in custom.scss:

.navbar {
  background-color: #003da5 !important;  /* UCR blue */
}

Google Search Console

The site is verified with Google Search Console via a meta tag in _quarto.yml:

format:
  html:
    include-in-header:
      text: |
        <meta name="google-site-verification" content="YOUR_CODE">

Do not remove this tag — removing it loses Search Console verification.

Sitemap is submitted at: https://girke.bioinformatics.ucr.edu/sitemap.xml

All project repos (GEN242 etc.) inherit verification from this root domain automatically — no separate verification needed for those.

Troubleshooting

Site not updating after push

Check the Actions tab for build errors. If the build succeeded but the site looks old, hard-refresh the browser (Ctrl+Shift+R).

Custom domain lost after deploy

If girke.bioinformatics.ucr.edu stops working, check: 1. The CNAME file exists in the repo root 2. GitHub Pages settings show the custom domain — Settings → Pages 3. The CNAME is listed under resources: in _quarto.yml so it gets copied to docs/ on every build:

project:
  resources:
    - CNAME

Dark mode icons invisible

If the toggle or search icons are not visible in dark or light mode, the fix is in custom.scss and custom-dark.scss — see the icon fix rules targeting a.quarto-color-scheme-toggle and div#quarto-search.

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