NCI Genomic Data Commons Access

transfer

R Documentation

Bulk data download

Description

The GDC maintains a special tool, https://docs.gdc.cancer.gov/Data_Transfer_Tool/Users_Guide/Getting_Started/, that enables high-performance, potentially parallel, and resumable downloads. The Data Transfer Tool is an external program that requires separate download. Due to recent changes in the GDC API, the transfer function now validates the version of the 'gdc-client' to ensure reliable downloads.

Usage

transfer(uuids, args = character(), token = NULL, overwrite = FALSE)

gdc_client_version_validate(valid_version = .GDC_COMPATIBLE_VERSION)

transfer_help()

Arguments

`uuids`	character() vector of GDC file UUIDs
`args`	character() vector specifying command-line arguments to be passed to `gdc-client`. See `transfer_help` for possible values. The arguments `--manifest`, `--dir`, and `--token-file` are determined by `manifest`, `destination_dir`, and `token`, respectively, and should NOT be provided as elements of `args`.
`token`	character(1) containing security token allowing access to restricted data. See https://gdc-docs.nci.nih.gov/API/Users_Guide/Authentication_and_Authorization/. Note that the GDC transfer tool requires a file for data transfer. Therefore, this token will be written to a temporary file (with appropriate permissions set).
`overwrite`	logical(1) default FALSE indicating whether existing files with identical name should be over-written.
`valid_version`	character(1) The last known version that works for the current data release for which to validate against, not typically changed by the end-user.

Value

character(1) directory path to which the files were downloaded.

Functions

gdc_client_version_validate(): If you are using the 'client' option, your 'gdc-client' should be up-to-date (>= 1.3.0).
transfer_help():

Examples

## Not run: 
uuids = files() %>% 
  filter(access == "open") %>% 
  results() %>%
  ids()
file_paths <- transfer(uuids)
file_paths
names(file_paths)
# and with authenication
# REQUIRES gdc_token 
# destination <- transfer(uuids,token=gdc_token())

## End(Not run)

Bioconductor/GenomicDataCommons documentation built on Jan. 30, 2024, 11:59 p.m.