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Download Google Bucket Inputs from a JSON

For a json containing gs:// bucket paths, for example:

{
    "input_file": {
        "class": "File",
        "path": "gs://topmed_workflow_testing/topmed_aligner/input_files/NWD176325.0005.recab.cram"
    },
    "reference_genome": {
        "class": "File",
        "path": "gs://topmed_workflow_testing/topmed_variant_caller/reference_files/hg38/hs38DH.fa"
    }
}

This script will:

  1. Download all google bucket files into the current directory (using gsutil).
  2. Output a new json modified to contain the new local paths.

To run:

python dl_gsfiles_frm_json.py <path-to-json-file>

If the path to this script is: /usr/local/bin/dl_gsfiles_frm_json.py then a convenient alias can be created in ~/.bashrc by adding:

gs_json() { python /usr/local/bin/dl_gsfiles_frm_json.py "$1"; }

Then simply run anytime using:

gs_json <path-to-json-file>