R/is_diamond_installed.R

In drostlab/rdiamond: Seamless Integration of DIAMOND2 Sequence Searches in R

is_diamond_installed <- function(diamond_exec_path = NULL) {
    # test if a valid DIAMOND version is installed
    tryCatch({
        if (!is.null(diamond_exec_path))
            # e.g. diamond_exec_path = '/opt/miniconda3/bin/'
            sys_out <-
            system(paste0(file.path(diamond_exec_path,"diamond version")), intern = TRUE)

        if (is.null(diamond_exec_path))
            # e.g. diamond_exec_path = '/opt/miniconda3/bin/'
            sys_out <-
                system("diamond version", intern = TRUE)

    }, error = function(e)
        stop(
            "It seems like you don't have DIAMOND2 installed locally on your machine or the PATH variable to the DIAMOND2 program is not set correctly.",
            " Please use the 'diamond_exec_path' argument to specify a path to your diamond excecutable, e.g. diamond_exec_path = '/usr/local/bin' or diamond_exec_path = '/opt/miniconda3/bin'.",
            call. = FALSE
        ))

    if (any(stringr::str_detect(sys_out, "diamond")))
        return(TRUE)

}