OTTR Course
Set Up

Download cheatsheet
Last updated: January 16, 2026

Log into GitHub or make a GitHub profile if you are new to GitHub

Go to github.com

Sign up for GitHub if you haven’t already - it’s free!

Make sure you are logged into GitHub - check at https://github.com/ - you should see your profile in the upper right corner

Create a repository from the OTTR_Template template

Go to OTTR_Template

In the upper right, click on:
Use this template

Make sure you don’t click on the green “Code” button instead!

Set your repo to “Public

Enable workflow actions

In your OTTR repository, go to Settings in the top navigation tabs settings gear icon

Go to Actions in the menu on the left side actions icon

Select General just below Actions

Scroll down to Workflow permissions

  1. Ensure Read and write permissions is selected

  2. Check Allow GitHub Actions to create and approve pull requests

  3. Click Save

Set up GitHub Pages

In your OTTR repository, go to Settings in the top navigation tabs settings gear icon

Go to Pages in the side navigation pages icon

In the Build and deployment section

  1. Under Source, select Deploy from a branch
  2. Under Branch, pick main and choose /docs, and click Save

at the bottom of the page, check Enforce HTTPS

Set up your GitHub personal access token

Click on your profile photo in the upper right profile photo icon

Scroll down to Settings settings gear icon

Scroll down in the menu on the left side to Developer Settings in the lower left side navigation settings gear icon

Scroll down in the left side menu on the left side to Personal access tokens personal access token icon

Select Tokens (classic)

Click very light gray button that says
Generate new token ▾

(upper right)

Select Generate new token (classic)

Confirm your access if you have two factor authentication set up (you will be asked to submit a code or something similar)

Name your token GH_PAT in the “Note” section

Note that your token will expire based on the date that you set in the Expiration section. You will have to complete this process again when your token expires. GitHub will let you know as you will get an error about credentials. It is a good idea to use the default settings.

Underneath Select Scopes (where the check boxes are), check repo (so everything under it is checked) and workflow

Click:
Generate token

Copy the personal access token copy icon and save somewhere safe and private. Please note that you cannot retrieve this personal access token again later from GitHub. If you lose it, you just need to complete this process again.


Click here to see GitHub documentation on creating a personal access token.

Save the copied personal access token as a repository secret

In your OTTR repository, go to Settings in the top navigation tabs settings gear icon

Note that this is different from your profile settings where you made your token.

Go to Secrets and variables in the side navigation secrets and variables icon

Click on Actions

Under Repository secrets, click on
New repository secrets

Under Name, enter GH_PAT

For Secret, paste your copied personal access token

Click on:
Add secret


Click here to see GitHub documentation on setting repository secrets.



Authors: Kate Isaac wrote the content and created the original styling, Carrie Wright did the css styling and Carrie Wright and Candace Savonen did the publishing engineering for the cheatsheet. Padmashri Saravanan and Allissa Dillman from BioDataSage worked with Carrie Wright to review and improve the cheatsheet. OTTR was created and or is maintained by the following team: Candace Savonen, Carrie Wright, Kate Isaac, Ava Hoffman, Adam Coffman, Katherine Cox, Federick Tan, John Muschelli, Howard Baek, and Jeffrey Leek.