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Workflows available

The BaseSpace_Fetch workflow facilitates the transfer of Illumina sequencing data from BaseSpace to a workspace on the Terra.bio platform. Data that has been transferred from an Illumina sequencer to BaseSpace is already in a cloud location. 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.

In order 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.

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

This process must be performed prior to using the BaseSpace_Fetch workflow the first time.

Setup Jupyter Cloud Environment

Install the BaseSpace Command Line Tool To Get The Access Token And API Server Address

Preparing to retrieve a run with BaseSpace_Fetch

<aside> 💡 Best Practices for Sample Identifiers

Avoid the use of underscores and whitespaces in the BaseSpace Project/Run name and/or the sample identifiers
- Underscores in a sample name will lead to BaseSpace_Fetch failure
Avoid re-using Sample IDs </aside>

Page Contents

Workflows available

Retrieving BaseSpace Access Credentials

Setup Jupyter Cloud Environment

Install the BaseSpace Command Line Tool To Get The Access Token And API Server Address

Preparing to retrieve a run with BaseSpace_Fetch

Prepare the metadata spreadsheet for the BaseSpace_Fetch workflow

Upload the metadata spreadsheet to the destination workspace in Terra.bio

Using BaseSpace_Fetch Workflow

Inputs

Steps

Outputs