Using Jira Cloud? See the corresponding article.

Integrate GitHub Enterprise with Jira Server

Quickly learn how to connect GitHub Enterprise git repositories via Git Integration for Jira Server.

What's on this page:

Creating a Personal Access Token

If two-factor authentication is enabled for your GitHub Enterprise account, you will need to create a PAT to access your git repositories. Enable two-factor authentication in your GitHub Enterprise account for increased security.

While instructions from GitHub works just fine, follow this article for some specific instructions to get you started.

Using Auto-Connect

This process requires an existing GitHub Enterprise account.

We recommend using the Auto-connect integration panel to connect multiple repositories from your GitHub Enterprise account.

1. On your Jira Server dashboard menu, go to Git → Manage repositories.

2. The git configuration page for connecting repositories is displayed.

3. On the Auto-connect integration panel, click GitHub Enterprise. The Auto-connect Wizard is displayed.

5. For the Host URL, enter the address of the GitHub Enterprise server.

6. Enter the Personal Access Token in the provided box as required.

For repository managers, collaborators or users that have enabled 2FA, enter username and the PAT as the password.

Configuring the Advanced settings is optional. However, admins/power users may set how the project listing is displayed.

Custom API Path – his is a relative path that starts with "/". The maximum allowed length is 2000 characters or less. The integration will use the relative REST API path to retrieve the list of tracked repositories. The Custom API Path is called everytime the list of repositories is loaded, on a regular scheduled reindex and a manual reindex. For more examples, see article Jira Server: Working with Custom API Path - GitHub Enterprise.

JMESPath filter – JMESPath is a query language for JSON used to filter API results and to limit which repositories are integrated. The maximum allowed length is 2000 characters or less. For help with writing expressions, please contact support. Read about JMESPath expressions on their website. For some other examples, see Jira Server: Working with JMESPath Filter in GitHub Enterprise.

Fetch refspec – Git refspecs contains patterns mapped as references from the remote to the local repository.
For more information, see Git Internals -- The Refspec.
1. The first two refspec options are required.
2. The rest of the options are OPTIONAL:
  1. Clone and index ref notes (refs/notes) – This is a reference to refs/notes/* used for fetching. This option is enabled by default. This affects git notes which are not shown:
    1. ...when refs/notes are disabled on connecting a repository.
    2. ...when a new note comes when refs/notes is disabled.
  2. Clone and index changes (refs/changes) – This is a reference to refs/changes/* used for fetching. This option is turned off by default.
  3. Clone and index other refs – This is a user-defined list of references used for fetching. It is a comma-separated list with the format:
    - +refs/refname1/*:refs/refname1/*, refs/refname2/*:refs/refname2/*, ...

While Custom API Path and JMESPath filter are mutually exclusive, you can use one, the other, both or neither.

7. Click Connect.

8. On the following screen, the Git Integration for Jira app will read all available repositories from your GitHub Enterprise account. Click Import repositories.

Repositories that are added or removed from GitHub Enterprise will be likewise connected or disconnected from Jira Server.

If your git url contains multiple repositories, it will be added as tracked repositories in the git configuration list. Otherwise, a git repository is added instead.

9. After the import process, the Settings dialog is displayed:

On the Integration Settings, setting the Require User PAT option to ON, will require users to provide PAT specific for branch and merge requests (via the developer panel» on the Jira issue page). For more information on this feature, see Integration Settings: Require User PAT ».
Set Smart Commits » and Repository Browser » to enable/disable these features.
Set Project Permissions according to your organization's project association rules. For detailed information, see Setting Project Permissions.

10. Click Finish.

GitHub Enterprise repositories are now connected to Jira Server.

Single Repository

Look for the the GitHub repository URL on the repository project page. Choose between SSH or HTTPS.

Use this information to connect the GitHub git repository to your Jira server via Git Integration for Jira app:

On your Jira dashboard menu, go to Git > Manage repositories.
Click Connect to Git Repository to open the Connect Wizard.
Paste the URL from GitHub Enterprise web portal in the provided box.
Continue to the next step by following the screen instructions.
Click Finish to complete this process.

The repository is now connected to Jira Server.

Setting Up GitHub Enterprise Permissions

We recommend using a "service user" in GitHub Enterprise (example: "GitIntegrationforJira") to be used to integrate with Git Integration for Jira app. This dedicated "service user" will allow the GitHub Enterprise administrator to set permissions so the app clones only the desired repositories.

Assign GitHub Enterprise permissions for team members or collaborators to allow which resources are accessible for service users. This feature is only available in a GitHub Organization.

Default Repository Permission

1. Login to your GitHub Enterprise account.

2. Go to Settings.

3. Under Organization settings, click Member Privileges.

Choose the default permission level for organization members.

The default repository permission only applies to organization members and not to outside collaborators. If the default permission is set to None, organization members will need to be given access to repositories using the Teams or Collaborators methods (see below).

4. Save the changes.

For more information, see Access Permissions on GitHub ».

Teams and Collaborators

To give a member additional access, they must be added to a team or make them collaborators on individual repositories.

Set default repository permission for the current team:

1. Open an organization team. (Your org > Team > scroll down to the bottom then click the desired team.)

2. Click the Repositories tab.

3. Set Read, Write or Admin repository access as desired.

Assign members to a team on your GitHub repository:

1. Create a team in your GitHub Organization.

2. Invite a member to add it into the team. An email invitation is sent to that GitHub service user.

The service user is then added to the team if the invitation has been accepted.

3. Click the service user to manage permissions for this member to:

Set desired Role for this member.
Convert this member to outside collaborator.
Give this member access to organization repositories.
Remove this member from the team.

4. Click Manage access to manage repository access for this member.

While users have configured PAT for repository access, users in a GitHub Enterprise must at least have Read permissions. This allows them to view commits and smart commits, and browse repositories (if enabled) of connected GitHub Enterprise repositories inside Jira.

For repository managers, collaborators and commit authors, set these users to have Write permissions. This will allow them to view commits and smart commits, browse repositories and also enables them to create branches and pull requests to specified GitHub git repositories via developer panel of a Jira issue.

The user PAT for "Require User PAT" setting should have Write permission. Otherwise, the user will not be able to use it for branch or pull request creation/deletion.

For more information on organization teams, see GitHub: Organizing Members into Teams ».

For more information on inviting collaborators, see Inviting Collaborators to a Personal/Organization Repository ».

Setting Up GitHub Web Links

The Git Integration for Jira app automatically configures web linking for GitHub Enterprise git repositories.

Viewing Git Commits in Jira Server

Perform a git commit by adding the Jira issue key in the commit message. This will associate the commit to the mentioned Jira issue.
Open the Jira issue.
Scroll down to the Activity panel then click the Git Commits tab.
Click View Full Commit to view the code diff.

Working with Branches and Pull Requests with GitHub

This process requires a GitHub Enterprise git repository and a PAT with repo scopes.

For GitHub Organization, the user must have the Write permissions and the repo PAT scopes.

Default Branch

Most git integrations allow changing of the default branch of the repository/project other than "master". This change is reflected in the Repository Settings of the Git Integration for Jira app on the next reindex. Auto-connected integrations support this feature where Git Integration for Jira app gets the default branch from almost all integrations and apply this setting at repository level.

Main branch for repositories within an integration can only be changed on the git server.

1. On your Jira Server, open a Jira issue. On the Jira developer panel under Git Source Code, click Create Branch.

2. The following dialog is displayed:

Select a Repository from the list.

If there are several repositories with the same name, the listed GitHub Enterprise repositories will have their names attached with a GitHub organization name. For example, BigBrassBand/second-webhook-test-repo.

Choose a Base branch.
Enter a Branch name or leave it as is (recommended).

If the Require User PAT option is enabled in the Integration Settings and a user PAT isn't configured yet for the selected repository via Repository Browser, the following dialog is displayed instead:

Click the link label to setup the PAT. This will show the Repository Browser listing connected git repositories.

Click
to setup a PAT for the selected repository. Paste a valid PAT of the current user to proceed. Invalid PATs will fail the branch creation process.
Click the
icon to use this PAT and save it to the current user profile. Otherwise, click the
icon on the right to cancel setting up PAT for this repository.
After the above steps have been taken, the users will be able to proceed with branch creation.

3. Click Create Branch. The newly-created branch is now listed in the developer panel under Branches.

Perform a commit to the newly-created branch to be ready for merge.

Pull Request

The pull request feature works the same as merge request.

To create a pull request and merge it to the main source (master):

1. On your Jira Server, open the Jira issue where your previously created a branch.

2. On the developer panel under Git Source Code, click Create Pull Request.

3. The following dialog is displayed:

Select a Repository from the list.

Choose the newly-created branch as the Source branch.
Set master as the Target branch.
Enter a descriptive title or leave it as is (recommended).

If an invalid PAT was configured for the selected repository, the pull request creation process will fail.

4. Click Create to create the pull request.

The pull request is listed on the developer panel of the Jira issue page.

The pull request is also ready for approval by the reviewers in your GitHub Enterprise web portal.