R/check_dep.R

In sunshanwen/BP4RNAseq: A babysitter's package for reproducible RNA-seq analysis

#' Check the existence of dependancies.
#'
#' Trim samples with adapter using cutadapt based on the results from quality_test().
#' @param dependancy the dependancy to check.
#' @export check_dep
#' @return TRUE if the dependancy exists, otherwise FALSE. 
#' @examples
#'
#' check_dep(dependancy = 'cutadapt')
#'

check_dep <- function(dependancy) {
    status <- tryCatch(system2(command = "which", args = dependancy, stdout = FALSE, stderr = FALSE), error = function(err) {
        1
    }, warning = function(war) {
        2
    })
    if (status == 0) 
        return(TRUE) else return(FALSE)
}