transfer {GenomicDataCommons} | 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. #' @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.

### Usage

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

    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.

### Value

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

### Functions

- `transfer_help`:

### Examples

    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)

[Package GenomicDataCommons version 1.14.0 Index]