How do I generate an Illumina BaseSpace Access Token?

To import files from BaseSpace into Tapestri Pipeline, customers must first generate an Access Token to authenticate their identity with the Illumina system. 

This article covers:

How do I generate a BaseSpace Access Token?

How do I connect Tapestri Pipeline to Illumina BaseSpace?

How do I import FASTQ files from BaseSpace?

How do I generate a BaseSpace Access Token? 

BaseSpace Access Tokens can be created from either the Command Line Interface (CLI) or the BaseSpace Developer Application: 

1. Authenticate the BaseSpace CLI – Follow these instructions to install and authenticate the CLI. Once you successfully authenticate yourself, the “.basespace” folder is created in the USER_HOME. Inside that is the file default.cfg that contains the Access Token.
2. Create a BaseSpace Developer App – Create an app to generate the Access Token. Use these steps to create your token:
1. Log into your BaseSpace account.
2. Click Apps in the main menu.
3. Click App Developer Portal on the Apps page.
4. In the top menu, click My Apps.
5. Follow the instructions to create a new app.
6. Once created, open the app, and go to the Credentials page to retrieve the Access Token.

Now that you created your Access Token, store it in a safe location for future access. 

How do I connect Tapestri Pipeline to Illumina BaseSpace? 

1. Log into Mission Bio Portal. 
2. Launch Tapestri Pipeline.
3. Go to the top-right corner and click your name. A drop-down menu will appear. Click Cloud Connector.
   
4. Paste your Access Token in the Illumina BaseSpace section and select the Region based on where your BaseSpace serves are located. Click Connect. For instructions on how to generate an access token, refer to this section.

After you connect Tapestri Pipeline to Illumina BaseSpace, you can import FASTQ files from BaseSpace. 

How do I import FASTQ files from BaseSpace? 

1. From the Runs or Files page of Tapestri Pipeline, click on Add Files.
2. Click on Import from Illumina BaseSpace. 
3. Input the Biosample Name. 
4. To define the Biosample Name, follow these steps:
   1. 1. Go to your Illumina BaseSpace application and log in. 
      2. Click the Projects tab. Click on the project you want to import into Tapestri Pipeline. 
      3. The number shown in the URL on your browser is the Project ID. For example, if the URL is https://basespace.illumina.com/projects/123456789, then the Project ID is 123456789. Copy this number. 
      4. Within your selected Project, click the Biosample tab.
      5. From the list of biosamples, find the name of the biosample you want to import, such as DNA001.
      6. The Biosample Name in the Tapestri Pipeline app has this format: Project ID:Biosample Name. Enter your Project ID and biosample name into the Biosample Name field. In our example, the biosample name would be 123456789:DNA001. The name should not contain spaces.
5. To import multiple samples of the same analyte, separate them with either a “,” or “;”.
6. To import both DNA and Protein FASTQ files, click the “+ Add FASTQ files for another analyte” text.
7. Click Import.