R/findFastqDump.R

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

findFastqDump <- function(...,
                          commandName='fastq-dump',
                          versionPattern=".*fastq-dump[ ]*:[ ]*([0-9.]+)",
                          verbose=FALSE)
{
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  # Aroma-specific variable
  path <- getExternalHome("FASTQDUMP_HOME")

  verbose && enter(verbose, "Locating FastqDump software")
  res <- findExternal(command=commandName, path=path, versionPattern=versionPattern, ...)
  res
} # findFastqDump()