R/findGATK.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

findGATK <- function(mustExist=TRUE, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'mustExist':
  mustExist <- Arguments$getLogical(mustExist)

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enter(verbose, "Locating GATK software")

  command <- "GATK"
  verbose && cat(verbose, "Command: ", command)

  # Check for cached results
  res <- .findCache(name=command)
  if (!is.null(res)) {
    pathname <- res$path
    verbose && cat(verbose, "Found cached result.")
    verbose && exit(verbose)
    return(pathname)
  }

  path <- Sys.getenv("GATK_HOME")
  verbose && printf(verbose, "System variable 'GATK_HOME': '%s'\n", path)
  if (path == "") path <- NULL

  if (is.null(path) || !isDirectory(path)) {
    if (mustExist) {
      throw(sprintf("Failed to located GATK home directory"))
    }
    return(NULL)
  }

  path <- Arguments$getReadablePath(path, mustWork=FALSE)
  verbose && cat(verbose, "Located directory: ", path)

  # Get main GATK jar file
  filename <- "GenomeAnalysisTK.jar"
  pathname <- Arguments$getReadablePathname(filename, path=path, mustExist=FALSE)
  verbose && cat(verbose, "Located main jar file: ", pathname)


  if (isFile(pathname)) {
    .findCache(name=command, path=pathname)
    ver <- systemGATK("--version", stdout=TRUE, stderr=TRUE)
    attr(pathname, "version") <- ver
    .findCache(name=command, path=pathname)
  } else if (mustExist) {
    throw(sprintf("Failed to located GATK tools"))
  }

  verbose && exit(verbose)

  pathname
} # findGATK()