Dockstore 1.9.0 provides users with a way to keep their workflows automatically updated (instead of needing to manually refresh) by using GitHub apps. Here, we will go over how to migrate your existing Dockstore workflows to use our GitHub App.
The first step to migrating a workflow is the same as adding a new workflow via GitHub Apps: install our Dockstore GitHub App in an organization or your personal account, if you have not already done so.
Once the GitHub app is installed and given access to the correct repository, the next step is to create a .dockstore.yml file. We'll cover a very straightforward example first, but depending on how you configured the workflow during registration and whether your GitHub repository houses multiple workflows published on Dockstore, there will be additional steps to writing your .dockstore.yml file.
Let's say we have the following CWL workflow registered on Dockstore that came from this repository and you would like to convert the master branch.
As noted in our other documentation, create a .dockstore.yml file in the root directory of the branch you want to migrate (in this example, it's the master branch) in your repository. The file should look like the following
version: 1.2
workflows:
- subclass: CWL
primaryDescriptorPath: /Dockstore.cwl
testParameterFiles:
- /test/dockstore.cwl.json
topic: A short description of the workflow
The information above was filled out using the following:
subclass
is taken from theDescriptor Type
primaryDescriptorPath
is fromWorkflow Path
testParameterFiles
is fromTest File Path
topic
is a short text description of the workflow, 150 characters or less.
During the original registration for your workflow, you may have filled out the Workflow Name
field shown in the picture below.
To check if the workflow you want to migrate has a workflow name set, select the workflow and look at the title on top, seeing if it has a fourth component to its title. As mentioned above, if you see a workflow name inserted, you must include the name field in your .dockstore.yml file.
version: 1.2
workflows:
- subclass: CWL
primaryDescriptorPath: /Dockstore.cwl
testParameterFiles:
- /test/dockstore.cwl.json
name: optional-name
topic: A short description of the workflow
If you have multiple workflows registered on Dockstore that stem from the same GitHub repo, a single .dockstore.yml can be used to convert them. Again, you need to check for the Workflow Name field being set because it's needed for multi workflow repositories. If the name field in the dockstore.yml
doesn't match the Workflow Name field in Dockstore, the migration of your workflow on Dockstore will not go through and it will instead create a new Dockstore entry. Let's say we want to convert these two workflows that come from this repository.
Your .dockstore.yml would look like the following:
version: 1.2
workflows:
- subclass: CWL
primaryDescriptorPath: /Dockstore.cwl
testParameterFiles:
- /test/dockstore.cwl.json
topic: A short description of the unnamed workflow
- subclass: WDL
primaryDescriptorPath: /Dockstore.wdl
testParameterFiles:
- /test/dockstore.wdl.json
name: optional-name
topic: A short description of the workflow optional-name
Note
Push events will only be captured by Dockstore after installing the GitHub app onto the repo.
To test out your GitHub app integration, make a push to a branch. Navigate to or refresh your browser on the My Workflows page, and select the workflow you wanted to convert. You should see that the Workflow Information
section looks a bit different.
It now lists the mode as Automatically synced via GitHub App
instead of Full
, and information about paths is no longer included. You are also no longer able to refresh or restub the workflow any more. Since you can't refresh the entire workflow anymore, new versions from GitHub (releases/branches) that you want to add to Dockstore must have a .dockstore.yml file. However, you can still refresh already existing versions/branches on Dockstore that you haven't converted by going to the Versions tab, clicking Actions, and selecting Refresh Version.
Troubleshooting and FAQ <github-apps-troubleshooting-tips>
- tips on resolving Dockstore GitHub App issues.