Downloading Data from BaseSpace

  1. 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
  1. Get the Project ID for your run using the bs list command.
bs list projects
  1. Download your fastq files using the bs download command.
bs download project -i 112983871 -o CHMI_FFPE_RUN1_fastqs