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A command-line utility to upload VCF's using the Ingenuity Datastream API.

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usage: ingutil [-h] {upload,status} ...

Upload a VCF file to Ingenuity or check the status of an upload.

positional arguments:
  {upload,status}
    upload         Upload a VCF file to Ingenuity. API key, API secret,
                   activation code, and shared users are read from a JSON
                   file.
    status         Checks the status of an upload.

optional arguments:
  -h, --help       show this help message and exit



usage: ingutil upload [-h] [-c CONFIG_FILE] [-d DISPLAY_NAME] [-t]
                      vcf_file sample_name

positional arguments:
  vcf_file              input VCF file to upload, accepts .vcf or .vcf.gz
  sample_name           sample name (e.g. case0017)

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG_FILE, --config_file CONFIG_FILE
                        configuration file in JSON format (default: conf-
                        nosharing-noactivation.json)
  -d DISPLAY_NAME, --display_name DISPLAY_NAME
                        Barcode and Display Name in Ingenuity (default: same
                        as sample name)
  -t, --test            create metadata files only



usage: ingutil status [-h] [-c CONFIG_FILE] status_url

positional arguments:
  status_url            the status URL to check

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG_FILE, --config_file CONFIG_FILE
                        configuration file in JSON format (default: conf-
                        nosharing-noactivation.json)