Accessing Built in Help
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,settings} ...
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,settings}
for more information, specify -h after a command
download download data from the GDC
upload upload data to the GDC
settings display default settings
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,settings} ...
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]
[--color_off] [-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]
[--latest] [--config FILE] [-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
--color_off Disable colored output
-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 md5sums and/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, -c 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
--latest Download latest version of a file if it exists
--config FILE Path to INI-type config file
-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]
[--log-file LOG_FILE]
[--color_off] [-t TOKEN_FILE]
[--project-id PROJECT_ID]
[--path path]
[--upload-id UPLOAD_ID]
[--insecure] [--server SERVER]
[--part-size PART_SIZE]
[--upload-part-size UPLOAD_PART_SIZE]
[-n N_PROCESSES]
[--disable-multipart] [--abort]
[--resume] [--delete]
[--manifest MANIFEST]
[--config FILE]
[file_id [file_id ...]]
positional arguments:
file_id The GDC UUID of the file(s) to upload
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
--color_off Disable colored output
-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
DEPRECATED in favor of [--upload-part-size]
--upload-part-size UPLOAD_PART_SIZE, -c UPLOAD_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
--config FILE Path to INI-type config file