Help Menus

The GDC Data Transfer Tool comes with built-in help menus. These menus are displayed when the GDC Data Transfer Tool is run with flags -h or --help for any of the main arguments to the tool. Running the GDC Data Transfer Tool without argument or flag will present a list of available command options.

gdc-client --help
usage: gdc-client [-h] [--version] {download,upload,interactive} ...

The Genomic Data Commons Command Line Client

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

commands:
  {download,upload,interactive}
                        for more information, specify -h after a command
    download            download data from the GDC
    upload              upload data to the GDC
    interactive         run in interactive mode
The available menus are provided below.

Root menu

The GDC Data Transfer Tool displays the following output when executed without any arguments.

gdc-client
usage: gdc-client [-h] [--version] {download,upload,interactive} ...
gdc-client: error: too few arguments

Download help menu

The GDC Data Transfer Tool displays the following help menu for its download functionality.

gdc-client download --help
usage: gdc-client download [-h] [--debug] [--log-file LOG_FILE]
                                  [-t TOKEN_FILE] [-d DIR] [-s server]
                                  [--no-segment-md5sums] [--no-file-md5sum]
                                  [-n N_PROCESSES]
                                  [--http-chunk-size HTTP_CHUNK_SIZE]
                                  [--save-interval SAVE_INTERVAL]
                                  [--no-verify] [--no-related-files]
                                  [--no-annotations] [--no-auto-retry]
                                  [--retry-amount RETRY_AMOUNT]
                                  [--wait-time WAIT_TIME] [-u] [-m MANIFEST]
                                  [file_id [file_id ...]]

positional arguments:
  file_id               The GDC UUID of the file(s) to download

optional arguments:
  -h, --help            show this help message and exit
  --debug               Enable debug logging. If a failure occurs, the program
                                                          will stop.
  --log-file LOG_FILE   Save logs to file. Amount logged affected by --debug
  -t TOKEN_FILE, --token-file TOKEN_FILE
                        GDC API auth token file
  -d DIR, --dir DIR     Directory to download files to. Defaults to current dir
  -s server, --server server
                      The TCP server address server[:port]
  --no-segment-md5sums  Do not calculate inbound segment md5sumsand/or do not
                      verify md5sums on restart
  --no-file-md5sum      Do not verify file md5sum after download
  -n N_PROCESSES, --n-processes N_PROCESSES
                        Number of client connections.
  --http-chunk-size HTTP_CHUNK_SIZE
                        Size in bytes of standard HTTP block size.
  --save-interval SAVE_INTERVAL
                        The number of chunks after which to flush state file.
                        A lower save interval will result in more frequent
                        printout but lower performance.
  --no-verify           Perform insecure SSL connection and transfer
  --no-related-files    Do not download related files.
  --no-annotations      Do not download annotations.
  --no-auto-retry       Ask before retrying to download a file
  --retry-amount RETRY_AMOUNT
                        Number of times to retry a download
  --wait-time WAIT_TIME
                        Amount of seconds to wait before retrying
  -u, --udt             Use the UDT protocol.
  -m MANIFEST, --manifest MANIFEST
                        GDC download manifest file

Upload help menu

The GDC Data Transfer Tool displays the following help menu for its upload functionality.

gdc-client upload --help
usage: gdc-client upload [-h] [--debug] [-v] [--log-file LOG_FILE]
                         [-T TOKEN | -t TOKEN] [-H HOST] [-P PORT]
                         [--project-id PROJECT_ID] [--identifier IDENTIFIER]
                         [--path path] [--upload-id UPLOAD_ID] [--insecure]
                         [--server SERVER] [--part-size PART_SIZE]
                         [-n N_PROCESSES] [--disable-multipart] [--abort]
                         [--resume] [--delete] [--manifest MANIFEST]

optional arguments:
  -h, --help            show this help message and exit
  --debug               Enable debug logging.  If a failure occurs, the program
                        will stop.
  --log-file LOG_FILE   Save logs to file. Amount logged affected by --debug
  -t TOKEN_FILE, --token-file TOKEN_FILE
                        GDC API auth token file
  --project-id PROJECT_ID, -p PROJECT_ID
                        The project ID that owns the file
  --path path, -f path  directory path to find file
  --upload-id UPLOAD_ID, -u UPLOAD_ID
                        Multipart upload id
  --insecure, -k        Allow connections to server without certs
  --server SERVER, -s SERVER
                        GDC API server address
  --part-size PART_SIZE, -ps PART_SIZE
                        Part size for multipart upload
  -n N_PROCESSES, --n-processes N_PROCESSES
                        Number of client connections
  --disable-multipart   Disable multipart upload
  --abort               Abort previous multipart upload
  --resume, -r          Resume previous multipart upload
  --delete              Delete an uploaded file
  --manifest MANIFEST, -m MANIFEST
                        Manifest which describes files to be uploaded
--identifier, -i      DEPRECATED