R/download_dbGaP.R

In waldronlab/HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project

#' @keywords internal
#'
#' @importFrom magrittr %>%
download_dbGaP <- function(dbGaP_repository_key, dbGaP_directory) {
    system.file("extdata/cart_DAR48406_201802201501.krt",
                package = "HMP16SData") %>%
        paste("prefetch", ., "--ngc", dbGaP_repository_key) %>%
        system()

    paste("vdb-decrypt", dbGaP_directory, "--ngc", dbGaP_repository_key) %>%
        system()
}