- If necessary, authenticate your BaseSpace account by using the bs authenticate command and then going to the provided link and entering your BaseSpace login and password. This will add a config file to your home directory: ~/.basespace/default.cfg
bs authenticate- Get the Project ID for your run using the bs list command.
bs list projects
- Download your fastq files using the bs download command.
bs download project -i 112983871 -o CHMI_FFPE_RUN1_fastqs