basespace-download is a tool for downloading FASTQ files from Illumina's BaseSpace cloud service. For some instruments, analysis happens (by default) in the cloud. This tool is for downloading that data for local processing and analysis. Thankfully, Illumina provides a good API for interacting with BaseSpace!


You must possess a valid app-token from BaseSpace in order to use this application. This is your method for authenticating with BaseSpace.

For more information on getting an app-token, see here:


   basespace-download [arguments...]
   -t           Application token from BaseSpace [$BASESPACE_APP_TOKEN]
   -s           Sample ID to download
   -p           Project ID to download (all samples)
   --dr         Dry-run (don't download files)
   --help, -h       show help
   --version, -v    print the version

Building from scratch

You need to have Go installed first. Next, you can retrieve the Go code and build it in one step:

go get

Next, you can copy the binary from $GOPATH/bin to anywhere in your $PATH.