transfer: Bulk data download
In GenomicDataCommons: NIH / NCI Genomic Data Commons Access

Description Usage Arguments Value Functions Examples

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.

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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 `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.

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)