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Downloading from BaseSpace

Downloading fastq files

  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 using the bs list command.
bs list projects
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  1. Download your fastq files using the bs download command.
bs download project -i 112983871 -o CHMI_FFPE_RUN1_fastqs
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Downloading Runs

  1. Authenticate as in step #1 above.
  2. Get the run ID using the bs list command.
bs list runs
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  1. Download your run using the bs download command.
sudo bs download run -i 290560439 -o 250214_A00901_1293_BH3MTCDSXF
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