transfer {GenomicDataCommons} | R Documentation |
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. #' @param gdc_client character(1) name or path to gdc-client
executable. The executable that is used is found through the
gdc_client
. See gdc_client
for details on how to set the executable path.
transfer(uuids, args = character(), token = NULL, overwrite = FALSE) transfer_help()
uuids |
character() vector of GDC file UUIDs |
args |
character() vector specifying command-line arguments to
be passed to |
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. |
character(1) directory path to which the files were downloaded.
transfer_help
:
file_manifest = files() %>% filter(~ access == "open") %>% manifest(size=10) manifest_file = tempfile() write.table(file_manifest,file=manifest_file,col.names=TRUE,row.names=FALSE,quote=FALSE) destination <- transfer(manifest_file) dir(destination) # and with authenication destination <- transfer(manifest_file,token=gdc_token)