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Storage Connections

Storage connections in ElemBio Cloud are a cloud storage integration for AVITI Systems to transfer sequencing data to a cloud storage bucket. ElemBio Cloud centrally manages the cloud storage connections for all connected systems.

ElemBio Catalyst supports a storage connection that Element hosts and manages on your behalf. The following providers also support storage connections.

Cloud Storage Data Upload​

Throughout a sequencing run, data continuously uploads to the selected storage location. For runs that use a cloud storage connection, AVITI OS streams data from the instrument directly to the cloud bucket. If you are using a provider with a full-service solution, such as ElemBio Catalyst or DNAnexus, the bucket is managed for you. If you are using a custom cloud service provider, such as AWS or GCS, you fully own and control your bucket.

The storage connection configuration in ElemBio Cloud provides the permissions to generate temporary credentials that let the instrument communicate with the bucket. If the network connection experiences a disruption, the instrument caches data and retries the upload until it succeeds.

Data Upload Diagram

Storage Connection Details​

Storage connection cards include a storage location link, settings, and other details. Information depends on the provider type.

  • Bucket Name: For AWS and GCS, provides the name of the cloud storage bucket with a link.
  • Prefix: For AWS and GCS, displays the object prefix for the storage location.
  • Region: For AWS, displays the bucket region.
  • Project: For DNAnexus, provides the associated project.
  • Run Upload Folder: For DNAnexus, displays the folder structure in the project for run upload data.
  • Enabled for Run Upload: Indicates the Use for Run Upload setting, which controls the availability of the storage connection on instruments associated with your organization.
    • If the setting appears with a green check mark, the storage connection is available on instruments.
    • If the setting does not appear, the storage connection is unavailable on instruments. You can only use the storage connection as an output location for other ElemBio Cloud features, such as verified flows.
  • Enabled for Data Exploration: Indicates the Use for Data Exploration setting, which controls the availability of the storage connection in data browsers.
    • If the setting appears with a green check mark, the storage connection is available for data browsing.
    • If the setting does not appear, the storage connection is unavailable for data browsing.

Storage Connection Statuses​

A badge on storage connection cards indicates one of the following connection statuses:

  • Connected: ElemBio Cloud successfully verifies the connection.
  • Unverified: ElemBio Cloud cannot verify the storage connection and the associated provider credentials. The storage connection is unavailable until the issue is resolved. To resolve, verify the storage connection and review any error messages.

Add a Storage Connection​

Only administrators can add a storage connection. Before you create a storage connection, you must first set up the provider for the storage connection and complete any provider requirements, including credentials. For more information on adding a provider and a storage connection, see the page for your provider:

Managing Storage Connections​

The following buttons on the storage connection cards allow you to manage connections. The available actions depend on your user permissions.

  • Edit: Modifies the storage connection settings.
    • Changes take effect immediately.
    • ElemBio Cloud restricts editing to the name field and settings, such as the Use for Run Upload and Use for Data Exploration options.
  • Delete: Removes the storage connection from ElemBio Cloud and all associated AVITI Systems.
    • ElemBio Cloud prohibits the deletion of a storage connection in use by an associated system.
    • When prompted, enter the name of the storage connection to confirm deletion. Upon confirmation, ElemBio Cloud deletes the storage connection.
  • Manage Data Access: Grant read-only access to data through AWS bucket IAM policies. For AWS and ElemBio Catalyst storage connections only.
  • Set As Default: Makes a storage connection the default selection in run setup for AVITI Systems associated with the organization.
    • A badge on a storage connection card identifies the current default selection.
    • If you set a default but want to use a different storage connection for a run, you can manually make the change during run setup.
    • The storage connection default set in AVITI OS can override the default set in ElemBio Cloud.
  • Verify: Verifies the permissions for data transfers.
    • If the storage connection is connected, a green success message appears.
    • If a red error message appears, review the error message to address the issue.
    • For additional verification, access the ConnectionTest folder in the storage location and make sure the elembio-read-write.txt file shows a successful verification date.
  • View Associated Runs: Shows a list of runs that use the storage connection for output files.
Caution

If you disable the Use for Run Upload setting while editing a storage connection, the connection immediately becomes unavailable on associated instruments. Before disabling the setting, make sure that the change does not impact any in-progress instrument activities.

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