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Documentation Index

Fetch the complete documentation index at: https://docs.mantlebio.com/llms.txt

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Mantle simplifies code reusability and supports developer best practices by allowing you to connect directly to your public and private GitHub repositories.
  • Manage GitHub connections seamlessly in Mantle.
  • Access connected GitHub repos directly within Mantle Notebooks.
  • Add custom Nextflow pipelines from connected GitHub repos.*

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How to connect a GitHub repository to Mantle

The Mantle GitHub integration allows you to connect any of your private repositories so that you can access the contents in Mantle.
1

Add a new GitHub integration

  • Navigate to the Integrations tab within Mantle and scroll down to the Add a New Integration section.
  • Click on the GitHub card.
2

Fill out the form that appears and click the Add Integration button

  • Enter the name you want to use to refer to the repo in Mantle.
  • Enter the repo URL in the following format: github.com/<resource-owner>/<repo-name>.
  • Enter a GitHub token that enables read access to the repo. See below for instructions on how to generate this token.

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How to generate a GitHub token

To give Mantle read access to your GitHub repo, you will provide a GitHub token.
1

Navigate to the token settings in your GitHub account

Go to the Fine-grained tokens settings in GitHub.
2

In the top right corner, click the Generate new token button

3

Fill out the form that appears

  • Give the token a name.
  • Select the resource owner of the repo you are connecting to Mantle.
  • Set the expiration date. After this date, Mantle will no longer have access to your repo and you will need to generate a new token.
  • Select the repos you want the token to grant access to. We recommend creating one token per repo.
  • Scroll down to the Permissions section and expand the Repository permissions section.
  • Scroll down to the Contents section and set the Access level to Read-only.
  • Scroll all the way to the bottom of the page and click the Generate token button.
4

Copy and paste your token

  • Paste the token into the form for adding a new GitHub connection in Mantle.
The token will only be shown to you this time. You can store the token in a secure location, such as a password manager.

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How to access a connected GitHub repo in a Mantle Notebook

All of your connected GitHub repos are available from within Mantle Notebooks. When you start a Mantle Notebook, the connected repos will be cloned into your Notebook’s environment. Repos are stored within the github_repos directory in the root directory of all Notebooks. You can access the files within each repo at github_repos/<repo_name>. *Adding custom pipelines is available to professional and enterprise users. Contact us to learn more.