R/install_chocophlan.R

In kstagaman/sharpton-lab-metaGTx.processing: Sharpton Lab Metagenomic & Metatranscriptomic Processing

#' @name install.chocophlan
#' @title Install Chocophlan Database
#' @description This function installs the chocophlan database for using with Humann3.
#' @param location character; path to install location.
#' @seealso \code{\link{system}}, \code{\link{list2}}
#' @export

install.chocophlan <- function(location) {
  cmd <- paste("humann_databases --update-config yes --download chocophlan full", location)
  system(cmd)
}