Bundles
Bundles are curated data sets which combine assets such as pipelines, tools, and Base query templates. This is where you will find packaged assets such as Illumina-provided pipelines and sample data. You can create, share and use bundles in projects of your own tenant as well as projects in other tenants.
The following ICA assets can be included in bundles:
Data (link / unlink)
Samples (link / unlink)
Reference Data (add / delete)
Pipelines (link/unlink)
Tools and Tool images (link/unlink)
Base tables (read-only) (link/unlink)
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.
Some bundles come with additional restrictions such as disabling bench access or internet access when running pipelines to protect the data contained in them. When you link these bundles, the restrictions will be enforced on your project. Unlinking the bundle will not remove the restrictions.
You can not link bundles which come with additional restrictions to externally managed projects.
As of ICA v.2.29, the content in bundles is linked in such a way that any updates to a bundle are automatically propagated to the projects which have that bundle linked.
If you have created bundle links in ICA versions prior to ICA v2.29 and want to switch them over to links with dynamic updates, you need to unlink and relink them.
Linking an Existing Bundle to a Project
From the main navigation page, select Projects > your_project > Project Settings > Details.
Click the Edit button at the top of the Details page.
Click the + button, under Linked bundles.
Click on the desired bundle, then click the +Link Bundles button.
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). Any updates to the assets will be automatically available in the destination project.
To unlink a bundle from a project,
Select Projects > your_project > Project Settings > Details.
Click the Edit button at the top of the Details page.
Click the (-) button, next to the linked bundle you wish to remove.
Bundles and projects have to be in the same region in order to be linked. Otherwise, the error The bundle is in a different region than the project so it's not eligible for linking will be displayed.
Create a New Bundle
To create a new bundle and configure its settings, do as follows.
From the main navigation, select Bundles.
Select + Create .
Enter a unique name for the bundle.
From the Region drop-down list, select where the assets for this bundle should be stored.
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 (unless non-deprecated versions of the bundle exist). Select "Show deprecated bundles" to show all deprecated bundles. Bundles can not be recovered from deprecated status.
[optional] Configure the following settings.
Categories—Select an existing category or enter a new one.
Short Description—Enter a description for the bundle.
Metadata Model—Select a metadata model to apply to the bundle.
Enter a release version for the bundle and optionally enter a description for the version.
[Optional] Links can be added with a display name (max 100 chars) and URL (max 2048 chars).
Homepage
License
Links
Publications
[Optional] Enter any information you would like to distribute with the bundle in the Documentation section.
Select Save.
There is no option to delete bundles, they must be deprecated instead.
Edit an Existing Bundle
To make changes to a bundle:
From the main navigation, select Bundles.
Select a bundle.
Select Edit.
Modify the bundle information and documentation as needed.
Select Save.
Adding Assets to a Bundle
To make changes to a bundle:
Select a bundle.
On the left-hand side, select the type of asset (such as Flow > pipelines, Base > Tables or Bench > Docker Images) you want to add to the bundle.
Depending on the asset type, select add or link to bundle.
Select the assets and confirm.
Assets must meet the following requirements before they can be 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
completestate.
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.
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. All users wich currently have access to a bundle will automatically have access to the new version as well.
From the main navigation, select Bundles.
Select a bundle.
Select + Create new Version.
Make updates as needed and update the version number.
Select Save.
When you create a new version of a bundle, it will replace the old version in your list. To see the old version, open your new bundle and look at Bundles > your_bundle > Details > Versioning. There you can open the previous version which is contained in your new version.
Assets such as data which were added in a previous version of your bundle will be marked in green, while new content will be black.
Add Terms of Use to a Bundle
From the main navigation, Select Bundles > your_bundle > Bundle Settings > Legal.
To add Terms of Use to a Bundle, do as follows:
Select + Create New Version.
Use the WYSIWYG editor to define Terms of Use for the selected bundle.
Click Save.
[Optional] Require acceptance by clicking the checkbox next to 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.
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 reaccept the terms of use. When reacceptance is required, users need to reaccept the terms in order continue using this bundle in their pipelines. This is indicated when they want to enter projects which use this bundle.
Collaborating on a Bundle
If you want to collaborate with other people on creating a bundle and managing the assets in the bundle, you can add users to your bundle and set their permissions. You use this to create a bundle together, not to use the bundle in your projects.
From the main navigation, select Bundles > your_bundle > Bundle Settings > Team.
To invite a user to collaborate on the bundle, do as follows.
To add a user from your tenant, select Someone of your tenant and select a user from the drop-down list.
To add a user by their email address, select By email and enter their email address.
To add all the users of an entire workgroup, select Add workgroup and select a workgroup from the drop-down list.
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.
Viewer: view content without editing rights.
Contributor: view bundle content and link/unlink assets.
Administrator: full edit rights of content and configuration.
Repeat as needed to add more users.
Users are not officially added to the bundle until they accept the invitation.
To change the permissions role for a user, select the Bundle Role drop-down list for the user and select a new role.
To revoke bundle permissions from a user, select the trash icon for the user.
Select Save Changes.
Sharing a Bundle
Once you have finalized your bundle and added all assets and legal requirements, you can share your bundle with other tenants to use it in their projects.
Your bundle must be in released status to prevent it from being updated while it is shared.
Go to Bundles > your_bundle > Edit > Details > Bundle status and set it to Released.
Save the change.
Once the bundle is released, you can share it. Invitations are sent to an individual email address, however access is granted and extended to all users and all workgroups inside that tenant.
Go to Bundles > your_bundle > Bundle Settings > Share.
Click Invite and enter the email address of the person you want to share the bundle with. They will receive an email from which they can accept or reject the invitation to use the bundle. The invitation will show the bundle name, description and owner. The link in the invite can only be used once.
You can follow up on the status of the invitation on the Bundles > your_bundle > Bundle Settings > Share page.
If they reject the bundle, the rejection date will be shown. To re-invite that person again later on, select their email address in the list and choose Remove. You can then create a new invitation. If you do not remove the old entry before sending a new invitation, they will be unable to accept and get an error message stating that the user and bundle combination must be unique. They can also not re-use an invitation once it has been accepted or declined.
If they accept the bundle, the acceptance date will be shown. They will in turn see the bundle under Bundles > Entitled bundles. To remove access, select their email address in the list and choose Remove.
Entitled Bundles
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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