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Running Sracp

Saul A Kravitz edited this page Jun 20, 2018 · 4 revisions

Access the help with sracp help:

Usage:
  sracp [flags]
  sracp [command]

Available Commands:
  help        Help about any command
  version     Print the version number of sracp

Flags:
  -a, --accession string   A list of accessions to mount or path to cart file. ["SRR123,SRR456" | local/cart/file | https://<bucket>.<region>.s3.amazonaws.com/<cart/file>].
                           Environment Variable: [$DBGAP_ACCESSION]
      --aws-batch int      ADVANCED: Adjust the amount of accessions put in one request to the SDL API when using an AWS location.
                           Environment Variable: [$DBGAP_AWS-BATCH] (default 50)
  -d, --debug              Enable debug output.
  -e, --endpoint string    ADVANCED: Change the endpoint used to communicate with SDL API.
                           Environment Variable: [$DBGAP_ENDPOINT] (default "https://www.ncbi.nlm.nih.gov/Traces/sdl/1/retrieve")
  -f, --filetype string    comma separated list of the only file types to copy.
                           Environment Varible: [$DBGAP_FILETYPE]
      --gcp-batch int      ADVANCED: Adjust the amount of accessions put in one request to the SDL API when using a GCP location.
                           Environment Variable: [$DBGAP_GCP-BATCH] (default 25)
  -h, --help               help for sracp
  -l, --location string    Cloud provider and region where files should be located: [cloud.region].
                           Environment Variable: [$DBGAP_LOCATION]
  -n, --ngc string         A path to an ngc file used to authorize access to accessions in DBGaP: [local/ngc/file | https://<bucket>.<region>.s3.amazonaws.com/<ngc/file>].
                           Environment Variable: [$DBGAP_NGC]

Use "sracp [command] --help" for more information about a command.

Most of the options and environment variables are intended for advanced users and debugging. The only options intended for regular use by users are for passing the ngc file and specifying the list of accessions.

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