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, which can make retrieval difficult. Thankfully, Illumina provides a good API for interacting with BaseSpace. This tool makes downloading files for a particular sample or project very simple.
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: https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
USAGE: basespace-download [arguments...] 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 github.com/compgen-io/basespace-download
Next, you can copy the binary from $GOPATH/bin to anywhere in your $PATH.