Overview

The BaseSpace_Fetch workflow facilitates the transfer of Illumina sequencing data from BaseSpace (a cloud location) to a workspace on the Terra.bio platform. Rather than downloading the files to a local drive and then re-uploading them to another location, we can perform a cloud-to-cloud transfer with the BaseSpace_Fetch workflow.

Some initial set-up is required to use the workflow. To access one’s BaseSpace account from within a workflow on Terra.bio, it is necessary to retrieve an access token and the API server address using the BaseSpace command line tool. The access token is unique to a BaseSpace account. If it is necessary to transfer data from multiple BaseSpace accounts, multiple access tokens will need to be retrieved. Please see the “Retrieving BaseSpace Access Credentials” section below.

In this document, we provide instructions for both the retrieval of the BaseSpace access token and running the BaseSpace_Fetch workflow.

Retrieving BaseSpace Access Credentials

Preparing to retrieve a run with BaseSpace_Fetch

Using the BaseSpace_Fetch Workflow

Inputs

Outputs

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