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DNAnexus

ElemBio Cloud integrates with DNAnexus as a cloud service provider. The DNAnexus provider supports storage connections, compute activities, and verified flows, such as the Bases2Fastq flow. DNAnexus offers a suite of analysis options, including the Bases2Fastq app and options for secondary analysis. For an example workflow configuration, see the Integrating DNAnexus for FASTQ Automation tutorial.

Requirements​

Configuration of a DNAnexus provider requires the following components:

  • A DNAnexus project: The project stores run files output from the AVITI System.
  • An API token with access to the project: The API token serves as a credential for ElemBio Cloud to transfer data.

For more information on these requirements, see the User Interface Quickstart and Authentication pages in the DNAnexus Documentation.

Configuring ElemBio Cloud​

After fulfilling the provider requirements, you can complete the following tasks to configure ElemBio Cloud. The available actions depend on your user permissions.

Add a DNAnexus Provider​

  1. On the Providers page, select DNAnexus.
  2. Enter a unique name.
  3. Enter the API token for the DNAnexus project.
  4. Select Save to create the provider.
  5. The DNAnexus provider will automatically make a compute connection in ElemBio Cloud.

Add a DNAnexus Storage Connection​

A storage connection enables you to transfer data to the DNAnexus project you own. Before you create a storage connection, you must set up the provider.

  1. On the Storage page, select Add Storage.
  2. Select the DNAnexus provider for the storage connection.
  3. Enter a unique name.
  4. Enter the Project ID.
  5. If applicable, enter a Run Upload Folder to indicate a folder structure for run data.
  6. Select a Use for Run Upload setting.
    • If you enable the setting, the storage connection becomes available on instruments associated with your organization.
    • If you disable the setting, the storage connection is unavailable on instruments. You can only use the storage connection for ElemBio Cloud activities, such as verified flows.
  7. Select Save.

Add a DNAnexus Compute Connection​

When adding a DNAnexus provider, a compute connection is automatically created on your behalf by ElemBio Cloud. If you delete that connection, you can create anothe rby doing the following:

  1. On the Compute Connections page, select Add Compute.
  2. Select the DNAnexus provider for the compute connection.
  3. Enter a unique name.
  4. Select Save to add the compute connection.

Add a DNAnexus Bases2Fastq Flow​

Before setting up a DNAnexus Bases2Fastq flow in ElemBio Cloud, you will need the Workflow ID for the intended workflow in your DNAnexus project. The workflow allows you to execute Bases2Fastq and other analyses. Make sure to note the workflow ID, which the DNAnexus user interface displays when you select a workflow.

For help createing a DNAnexus workflow, follow the Integrating DNAnexus for FASTQ Automation tutorial.

To create a DNAnexus Bases2Fastq flow, follow the Add Assignment Flow instructions.

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