Register a Tool on Dockstore

Tutorial Goals

• Discover how to register a tool on Dockstore

• Publish your tool

Assumptions

This document assumes you have already have a tool ready to register. You do not need to have a Dockerfile associated with it unless you are using one our legacy registration methods (more on that below).

If you followed Getting Started With CWL to create a CWL tool, you will now have your Dockerfile and Dockstore.cwl in GitHub, have setup Quay.io to automatically build your Docker image, and have linked your accounts to Dockstore. This will allow you to use any of our registration methods, including legacy methods. Of course, you can always follow along with your own unique tools too, which may or may not be associated with an autobuilding Docker image.

Regardless of how you made your tool, this tutorial will assume you are using CWL. For all other languages, please see our documentation on workflows instead.

Note

The WDL community does not explicitly differentiate tools versus workflows. However, Dockstore allows the registration of “WDL tools” using legacy registration methods. We encourage people to register WDLs as workflows instead.

Register Your Tool in Dockstore

Note

You do not need an account to search for workflows on Dockstore or to launch them with our compute partners. However, to register content on Dockstore, you must have an account on Dockstore and link the necessary third-party accounts. Once this is done you can register workflows from the My Workflows page, tools from the My Tools page, or services from the My Services page.

There are a variety of ways to get your tools into Dockstore. Users can either use GitHub App registration or our legacy registration methods. GitHub App registration is the recommended way to register all new tools on Dockstore. GitHub App tools and tools registered using our other methods (legacy tools) are very different from one another. Use the following questions to determine which method to use:

• Registering a CWL CommandLineTool?

  • Hosted on GitHub?

    • Register your tool to automatically sync using GitHub Apps

  • Hosted on BitBucket or GitLab?

    • Register using legacy tool registration methods or consider uploading your work to GitHub

• Registering a CWL Workflow, WDL, Nextflow, or Galaxy descriptor files?

  • Hosted on GitHub?

    • Register your workflow to automatically sync using GitHub Apps

  • Hosted on BitBucket or GitLab?

    • Register using legacy workflow registration methods or consider uploading your work to GitHub

If you must use the legacy tool registration methods, then you may want to read Dockstore Tools Overhaul before continuing to the legacy methods described below.

Register Your Tool to Automatically Sync with GitHub (Recommended)

Note

You do not need an account to search for workflows on Dockstore or to launch them with our compute partners. However, to register content on Dockstore, you must have an account on Dockstore and link the necessary third-party accounts. Once this is done you can register workflows from the My Workflows page, tools from the My Tools page, or services from the My Services page.

Dockstore has added GitHub App support for registering tools. Using GitHub Apps, Dockstore can react to changes on GitHub as they are made, keeping Dockstore synced with GitHub automatically. You can read more about it in our docs about the Dockstore GitHub App, but a summary is present below.

Installing the GitHub App is simple. Navigate to /my-tools, /my-workflows, or /my-services using the drop down menu in the top right. In these screenshots, we will go via /my-tools, but the process is essentially the same for any of the other options.

Click the + button on the left hand sidebar.

A window will appear asking how you would like to register your tool, workflow, or service. Select Register using GitHub Apps.

Click + Manage Dockstore Installation on GitHub. You’ll then be redirected to GitHub where you can select which repositories can be accessed by the GitHub app.

You’ll then be redirected to GitHub where you can grant the app access to specific repositories within whatever organization you are installing into. Note that GitHub treats your username as its own “organization.” For instance, my GitHub username is aofarrel. If I want to install the GitHub App so it could access aofarrel/mycoolrepo, I would choose the first option here.

Install our GitHub App on either all repositories in an organization or on specific repositories

After selection of an organization, you can select whether to give access to all repositories or only select ones. If the organization you choose is intended to be just for Dockstore tools/workflows/services, you may want to allow access to all repositories. Otherwise, it is may be more intuitive to select only certain repositories. Click save and you will be taken back to the page you started on in Dockstore – either /my-tools, /my-workflows, or /my-services, depending where you started.

Important

The GitHub user who first adds a workflow onto Dockstore must correspond to a user on Dockstore.

You should now see the organization and the repositories you chose to keep track of in the “unpublished” tab. Here’s an example involving /my-services:

A note on permissions

If you are adding the GitHub App to an organization for which you are not an admin, GitHub may block your ability to install the app, even if you have maintainer access to the repository you are hoping to give the GitHub App permission to view. Please see this FAQ entry for more information.

See also

• Automatic Syncing with GitHub Apps and .dockstore.yml - details on writing a .dockstore.yml file

• Migrating Your Existing Workflows - a tutorial on converting already registered workflows

• Troubleshooting and FAQ - tips on resolving Dockstore Github App issues.

Ensuring sychronization

Once the GitHub App is installed and a .dockstore.yml is present, please make sure to push one additional commit to your repository. This helps make sure your workflows, tools, and services show up in Dockstore.

Once you’ve installed our GitHub app on a repository or organization, you’ll need to add a .dockstore.yml file to the root directory of a branch of the repository that contains your tool. This file contains information like tool path, test parameter file, tool name, etc. When a push is made or a tag is created on GitHub with a .dockstore.yml, Dockstore will add that branch to the corresponding tool on Dockstore. If the tool doesn’t already exist on Dockstore, one will be created (but will not automatically be published publically). Note that a single .dockstore.yml file can describe multiple tools, if all of those tools are in the same repository.

Below is a simple example of a .dockstore.yml file for an alignment tool to show you how easy it is to use. Note that all file paths in the file must be absolute.

version: 1.2
tools:
   - subclass: CWL
     primaryDescriptorPath: /aligner.cwl
     testParameterFiles:
     - /test/aligner.cwl.json

If you had our GitHub App installed on the repository myorg/alignments and then add the above .dockstore.yml to the develop branch, the following would occur.

• A CWL tool with the ID github.com/myorg/alignments will be created on Dockstore

• The version develop is added to the tool github.com/myorg/alignments

• The version has the primary descriptor file set to /aligner.cwl

• The version has one test parameter file: /test/aligner.cwl.json

Now that your tool has been added, any time there is a push to a branch on GitHub for this repository that has a .dockstore.yml, it is automatically updated on Dockstore! Anytime there is a deletion of a branch on GitHub that has a .dockstore.yml, the version is removed from Dockstore.

For more information on this method, as well as general troubleshooting advice, please check our Dockstore GitHub Apps Overview page.

Legacy Tool Registration

Important

The following methods are NOT recommended and should only be used if your tool descriptor files are registered on BitBucket or GitLab.

Important

Workflows and tools added to Dockstore via our legacy registration methods do not automatically stay in sync with their source repository. Instead, someone with access to the entries on Dockstore must periodically log into Dockstore and press a button to trigger a refresh. Although this process is quick and will bring in all new tags, commits, and branches with the click of a button, it is easy to forget to do this and might not be appropriate for frequently-updated tools and workflows. For this reason, we recommend using GitHub App registration instead.

If you are using BitBucket or GitLab and would prefer not to use GitHub, or if you are using GitHub but do not wish to install our app, our legacy registration methods have you covered. Several options are available to you and described in our legacy registration methods documentation.

Sharing Your Tool

After you have successfully added your tool onto Dockstore and have it synced with GitHub, Bitbucket, or GitLab, you are now ready to share your tool with the public! Assuming that your tool has at least one valid version, you can publish your tool for everyone to use. Simply select the tool on the /my-tool page and click publish.

Find Other Tools

You can find tools on the Dockstore website or also through the dockstore tool search command line option.

Next Steps

You can follow this basic pattern for each of your Docker-based tools. Once registered, you can send links to your tools on Dockstore to colleagues and use it as a public platform for sharing your tools.

Learn about Workflows and how they differ from tools.