I have created an organization on GitHub. My organization has some repos. These repos have API documentation that I would like to re-build and publish to gh-pages
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That's not possible currently, you can only create tokens for user accounts since user accounts have permissions associated with them (organizations don't). So, you'd need to create a token with an account which has access to the repository in question and give that to Travis. You can also create a machine account for that purpose.