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Bundles

You can use bundles to package assets such as sample data, pipelines, tools, and Base query templates, which you can use as a curated data set. You can share and use bundles in projects of your own tenant as well as projects in other tenants. Please note that there is a combined limit of 30 000 projects and bundles per tenant. You can include the following ICA assets in bundles:
  • Base tables (read-only)
  • Base query templates
  • Bench docker images
  • Data
  • Pipelines
  • Reference data
  • Sample data
  • Tools and Tool images
Assets must meet the following requirements before being added to a bundle:
  • For Samples and Data, the project the asset belongs to must have data sharing enabled.
  • The region of the project containing the asset must match the region of the bundle.
  • You must have permission to access the project containing the asset.
  • Pipelines and tools need to be in released status.
  • Samples must be available in a complete state.
The main Bundles screen has two tabs: My Bundles and Entitled Bundles. The My Bundles tab shows all the bundles that you are a member of. This tab is where most of your interactions with bundles occur. The Entitled Bundles tab shows the bundles that have been specially created by Illumina or other organizations and shared with you to use in your projects. See Access and Use an Entitled Bundle.

Create a New Bundle

To create a new bundle and configure its settings, do as follows.
  1. 1.
    From the main navigation, select Bundles.
  2. 2.
    Select New Bundle.
  3. 3.
    Enter a unique name for the bundle.
  4. 4.
    From the Bundle Location drop-down list, select where the assets for this bundle should be stored.
  5. 5.
    [Optional] Configure the following settings.
    • Categories—Select an existing category or enter a new one.
    • Status—Set the status of the bundle. When the status of a bundle changes, it cannot be reverted to a draft or released state.
      • Draft—The bundle can be edited.
      • Released—The bundle is released. Technically, you can still edit bundle information and add assets to the bundle, but should refrain from doing so.
      • Deprecated—The bundle is no longer intended for use. By default, deprecated bundles are hidden on the main Bundles screen. Select "Show deprecated bundles" to show all deprecated bundles. Bundles can not be recovered from deprecated status.
    • Short Description—Enter a description for the bundle.
    • Metadata Model—Select a metadata model to apply to the bundle.
  6. 6.
    Enter a release version for the bundle and optionally enter a description for the version.
  7. 7.
    [Optional] Links can be added with a display name and URL.
    • Homepage
    • License
    • Links
    • Publications
  8. 8.
    [Optional] Select the Documentation tab and enter any information you would like to attach to the bundle.
  9. 9.
    Select Save.
Note There is no option to delete bundles, they must be deprecated instead.

Edit Existing Bundle

To make changes to a bundle, do as follows.
  1. 1.
    From the main navigation, select Bundles.
  2. 2.
    Select a bundle.
  3. 3.
    Select Edit.
  4. 4.
    Modify the bundle information and documentation as needed.
  5. 5.
    Select Save.

Adding Assets to a Bundle

To make changes to a bundle, do as follows.
  1. 1.
    Select a bundle.
  2. 2.
    On the left-hand side, select the asset type under Flow (such as pipeline or tool) you want to add to the bundle.
  3. 3.
    Depending on the asset type, select add or link to bundle.
  4. 4.
    Select the assets and confirm.
When you link folders to a bundle, a warning is displayed indicating that, depending on the size of the folder, linking may take considerable time. The linking process will run in the background and the progress can be monitored on the Bundles > your_bundle > activity > Batch Jobs screen. To see more details and the progress, double-click the batch job and then double-click the individual item. This will show how many individual files are already linked.
Which batch jobs are visible as activity depends on the user role.
Project Creator
Project Collaborator same tenant
Project Collaborator different tenant
All batch jobs
All batch jobs
Only batch jobs of own tenant

Create a New Bundle Version

When creating a new bundle version, you can only add assets to the bundle. You cannot remove existing assets from a bundle when creating a new version. If you need to remove assets from a bundle, it is recommended that you create a new bundle.
  1. 1.
    From the main navigation, select Bundles.
  2. 2.
    Select a bundle.
  3. 3.
    Select Create new Version.
  4. 4.
    Make updates as needed.
  5. 5.
    Select Save.

Manage Bundle Users

To manage bundle users and their permissions, do as follows.
  1. 1.
    From the main navigation, select Bundles > your_bundle > Team.
  2. 2.
    To invite a user to collaborate on the bundle, do as follows.
    a. To add a user from your tenant, select Someone of your tenant and select a user from the drop-down list. b. To add a user by their email address, select By email and enter their email address. c. To add all the users of an entire workgroup, select Add workgroup and select a workgroup from the drop-down list. d. Select the Bundle Role drop-down list and choose a role for the user or workgroup.
    This role defines the ability of the user or workgroup to view or edit bundle settings.
    e. Repeat as needed to add more users.
    Users are not officially added to the bundle until they accept the invitation.
  3. 3.
    To change the permissions role for a user, select the Bundle Role drop-down list for the user and select a new role.
  4. 4.
    To revoke bundle permissions from a user, select the trash icon for the user.
  5. 5.
    Select Save Changes.

Linking an Existing Bundle to a Project

  1. 1.
    From the main navigation page, select Projects > your_project > Details.
  2. 2.
    Click the Edit button at the top of the Details page.
  3. 3.
    Click the + button, under LINKED BUNDLES.
  4. 4.
    Click on the desired bundle, then click the +Link Bundles button.
  5. 5.
    Click Save.
The assets included in the bundle will now be available in the respective pages within the Project (e.g. Data and Pipelines pages).

Add Terms of Use to a Bundle

  1. 1.
    From the main navigation, Select Bundles > your_bundle > Legal.
  2. 2.
    To add Terms of Use to a Bundle, do as follows:
    a. Select New Version. b. Use the WYSIWYG editor to define Terms of Use for the selected bundle. c. Click Save. d. [Optional] Require acceptance by clicking the checkbox, Acceptance required. Acceptance required will prompt a user to accept the Terms of Use before being able to use a bundle or add the bundle to a project.
  3. 3.
    To edit the Terms of Use, repeat Steps 1-3 and use a unique version name. If you select acceptance required, you can choose to keep the acceptance status as-is or require users to re-accept the terms of use.

Access and Use an Entitled Bundle

Entitled bundles are bundles created by Illumina or third parties for you to use in your projects. Entitled bundles can already be part of your tenant when it is part of your subscription. You can see your entitled bundles at Bundles > Entitled Bundles.
To use your shared entitled bundle, add the bundle to your project via Project Linking. Content shared via entitled bundles is read-only, so you cannot add or modify the contents of an entitled bundle. If you lose access to an entitled bundle previously shared with you, the bundle is unlinked and you will no longer be able to access its contents.
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