BaseSpace Automation Tasks

This repository contains Golden Helix server tasks for automating file downloads from Illumina BaseSpace.

Prerequisites

• Access to Illumina BaseSpace
• Valid BaseSpace account credentials

Setup Instructions

1. Get BaseSpace API Token

This step requires access to a Linux machine, but can also be done through the VSCode app on the Golden Helix server by going to Terminal > New Terminal and running the following commands:

1. Download the BaseSpace CLI tools from the BaseSpace CLI Overview

2. After installing the CLI tools, authenticate by running:

   cd ~
   wget -q "https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs" -O ./bs
   chmod u+x ./bs
   ./bs auth

3. You will be prompted to login to BaseSpace by copying and pasting the URL into your browser. Once logged in, the command will complete.

4. Retrieve the token from ~/.basespace/default.cfg. This token will be used as the "BaseSpace API key"

   cat ~/.basespace/default.cfg

The token will be displayed in the output. It will look like this:

apiServer   = https://api.basespace.illumina.com
accessToken = 9f5b6f49d1001a46e2c6fd791bfe791ce

Edit the basespace_project.task.yaml and basespace_biosample.task.yaml files and replace the basespace_access_token with the token you just retrieved.

If the API server in your default.cfg file is different from the default shown above, make sure to update the BASESPACE_API_SERVER variable in both task files to match your specific API server URL.

Tasks

The repository contains the following tasks:

Download BaseSpace Project Files (basespace_project.task.yaml)

Downloads files from a specific BaseSpace project.

Parameters:

• project: BaseSpace Project Name (example: 'MiniSeq: BRCA Panel')
• output_directory: Directory where files will be downloaded
• file_filter: Optional file extension filter (default: 'vcf.gz')
• basespace_access_token: Your BaseSpace API key

Download BaseSpace BioSample (basespace_biosample.task.yaml)

Downloads files for a specific BioSample from BaseSpace.

Parameters:

• bio_sample: BaseSpace BioSample Name (example: 'Veriti2-OBRCA-NA12878-20ng-rep4')
• output_directory: Directory where files will be downloaded
• file_filter: Optional file extension filter (default: 'vcf.gz')
• basespace_access_token: Your BaseSpace API key

Usage

1. Set up your BaseSpace API token as described in the Setup Instructions
2. Configure the task parameters in the respective YAML files:
   • Set the project name or biosample name
   • Specify the output directory
   • Optionally set a file filter

Notes

• The tasks will automatically download the BaseSpace CLI tools
• If multiple projects or biosamples match the specified name, the task will fail
• File filtering is optional - if not specified, all files will be downloaded
• The tasks require minimal resources (1 CPU core, 1GB memory)