R/helper.R

In luciorq/five: A Framework for Identification of Viral Elements

#' Check Docker
#'
#' Check if Docker API is available
#'
is_docker_available <- function(opt) {
  docker_available <- Sys.which("docker")
  if (isTRUE(docker_available != "")) {
    opt$docker <- TRUE
  } else {
    opt$docker <- FALSE
  }
  opt
}


#' Development Parameters
#'
#' Assign parameters for interactive testing during development
#'
#' @param opt
assign_test <- function(opt) {
  #Sys.setenv(PATH = paste("/edirect:/VelvetOptimiser-2.2.6:/CAP3",Sys.getenv("PATH"),sep = ":"))
  #Sys.getenv("PATH")
  #setwd("/temp_files/")
  #getwd()
  opt$fasta <- TRUE
  opt$input <- fs::path("library", "ERR555102.trimmed.fasta")
  opt$ref <- fs::path("reference_genome", "ixodes_scapularis-W1.fa")
  opt$bact <- fs::path("bacterial_genomes", "all_bacters.fasta")
  opt$nr <- fs::path("blast_nr", "nr")
  opt$nt <- fs::path("blast_nt", "nt")
  opt$adapter <- "TGGAATTCTCGGGTGCCAAGGAACTCCAGT"
  opt$threads <- "10"
  opt$si <- "21"
  opt$se <- "24"
  opt$hash <- "15"
  opt$deg <- TRUE
  opt$output <- base::paste0("five_results-", base::format(base::Sys.time(), "%Y%m%d"))
  opt$plot <- FALSE
  opt$sra <- FALSE
  opt
}

#' Function to print list based options as data frame
print_opt <- function(opt) {
  dplyr::data_frame(
    key = names(opt),
    value = unlist(opt)
  )
}