primerize.github.io

Static website for Primerize, hosted on GitHub Pages. Migrated from primerize.stanford.edu (Django/MySQL on AWS EC2) in May 2026.

Site structure

Plain HTML — no build step, no Jekyll, no framework.

index.html              # About / landing page
protocol/index.html     # Protocol (Sections 1–5)
code/index.html         # Code / download page
assets/
  css/
    bootstrap.min.css
    theme.css           # Custom navbar, colors, layout
    palette.css         # Label and panel color classes
    code.css            # Monospace / syntax highlight styles
  js/
    jquery.min.js
    bootstrap.min.js
  fonts/                # Glyphicon icon font (Bootstrap 3)
  images/
    docs/               # Protocol figures (JPG/SVG)
    ...                 # Site logo and background images
CNAME                   # Custom domain: primerize.stanford.edu

Previewing locally

No build step needed. Serve any directory with a static file server so that absolute paths (/assets/...) resolve correctly.

Python (simplest):

cd primerize.github.io
python3 -m http.server 8000
# open http://localhost:8000

Node (if you have it):

npx serve .

Check all three pages:

• http://localhost:8000/ — About
• http://localhost:8000/protocol/ — Protocol (verify plate images and section anchors)
• http://localhost:8000/code/ — Code

How GitHub Pages is configured

1. Repo is at github.com/DasLab/primerize.github.io.
2. In Settings → Pages, source is set to the main branch, root directory.
3. The CNAME file in the repo root contains primerize.stanford.edu. GitHub Pages reads this to serve the custom domain.
4. In Settings → Pages, "Enforce HTTPS" is enabled once the DNS record is in place.

Pushes to main deploy automatically (usually within 1–2 minutes).

DNS cutover (Stanford IT)

These steps point primerize.stanford.edu at GitHub Pages and decommission the AWS EC2 instance.

Prerequisites:

• Confirm the site looks correct at https://daslab.github.io/primerize.github.io/ first.
• Confirm CNAME file contains exactly primerize.stanford.edu (no trailing newline issues).

Steps:

1. Contact Stanford IT at ithelp@stanford.edu (or use the same DNS management portal used for daslab.stanford.edu) and request:

   • Remove the existing A or CNAME record for primerize.stanford.edu
   • Add a new CNAME record: primerize.stanford.edu → daslab.github.io

2. In GitHub Pages settings (Settings → Pages on this repo):

   • Set "Custom domain" to primerize.stanford.edu and save.
   • Once DNS propagates, the "Enforce HTTPS" checkbox will become available — enable it.

3. Verify (DNS propagation can take minutes to hours):

   dig primerize.stanford.edu CNAME
   # Should return: primerize.stanford.edu → daslab.github.io
   curl -I https://primerize.stanford.edu/protocol/#IDT
   # Should return HTTP 200 with cert for primerize.stanford.edu

   Also check these URLs in a browser:

   • https://primerize.stanford.edu/ — About page
   • https://primerize.stanford.edu/protocol/#IDT — scrolls to IDT anchor
   • https://primerize.stanford.edu/protocol/#temp_design
   • https://primerize.stanford.edu/code/

4. Terminate the AWS EC2 instance (IP 52.33.204.5) after DNS is confirmed working. SSH key is ~/.ssh/amazon.pem. Before terminating, make sure the archive in aws_archive/ is uploaded to DasLab Google Drive (see ../aws_archive/README.md).

Making changes

Edit HTML/CSS/JS directly and push to main. No compilation needed.

The plate diagrams in assets/images/docs/ are SVGs generated from JSON data in the Server_Primerize repo (media/images/docs/*.json). If the protocol plate data ever needs updating, regenerate them with the Python snippet in ../aws_archive/README.md.

Key inbound links to preserve

The Primerize documentation site links directly to these anchors — do not rename them:

URL	Anchor in protocol/index.html
/protocol/#temp_design	DNA Template Design
/protocol/#IDT	IDT Oligo Ordering
/protocol/#PCR	PCR Assembly
/protocol/#TX	In Vitro Transcription
/protocol/#par_prep	Massively Parallel Preparation