R/kmr_install_kmc.R

In c5sire/kmerize: K-Mer Tools for Building Databases

#' kmr_install_kmc
#'
#' Installs a local version of kmc3.
#'
#' @param download_file If provided, kmc3 is provided from a local archive.
#' User makes sure it is the appropriate version for the local OS.
#'
#' @return logical
#' @export
#' @family kmer_core
#'
#' @examples
#' if (interactive()) {
#'   kmr_install_kmc()
#' }
kmr_install_kmc <- function(download_file = NULL) {
  # check if installed locally on known path
  if (!is.null(download_file)) {
    tgt <- download_file
    if (!file.exists(tgt)) {
      stop("Path to archive does not exist!")
    }
  }

  kmc_ok <- check_install_ok()

  # get local OS ref
  los <- get_os()

  # get local kmc3 path reference
  kmc_dir <- get_kmc_dir()

  url_base <- "https://github.com/refresh-bio/KMC/releases/download/v3.0.0/"
  url_app <- switch(los,
    Windows = "KMC3.windows.tar.gz",
    Linux = "KMC3.linux.tar.gz",
    "KMC3.mac.tar.gz"
  )
  url <- file.path(url_base, url_app)
  # download from official URL the appropriate version
  tgt <- file.path(tempdir(), url_app) %>% get_safe_path()

  # if not installed and no package given
  if (!kmc_ok) {
    if (is.null(download_file)) {
      utils::download.file(url, tgt)
    }

    # unpack into known location
    utils::untar(tgt, exdir = kmc_dir)
  } else {
    message("KMC3 already installed locally.")
  }

  # check if program files present and works
  kmc_ok <- check_install_ok()
  stopifnot(kmc_ok)
  return(kmc_ok)
}