R/findPicard.R

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

findPicard <- 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 Picard software")

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

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

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

  if (!is.null(path) && isDirectory(path)) {
    path <- Arguments$getReadablePath(path, mustWork=FALSE)
    verbose && cat(verbose, "Located directory: ", path)

    # Validating
    files <- list.files(path=path, pattern="[.]jar$")
    if (length(files) == 0L) {
      throw("The located Picard directory contains no *.jar files: ", path)
    }

    # Validate by retrieving 'version' attribute.
    pathnameT <- file.path(path, "ViewSam.jar")
    verbose && enter(verbose, "Retrieving version")
    res <- systemJavaJar(pathnameT, "--version", stdout=TRUE, stderr=TRUE)
    ver <- res[1L]
    ver <- gsub("([0-9.-_]+).*", "\\1", ver)
    # Try to coerce
    tryCatch({
      ver <- package_version(ver)
    }, error = function(ex) {})
    attr(path, "version") <- ver
##    attr(pathname, "raw_version") <- res
    verbose && exit(verbose)

    .findCache(name=command, path=path)
  } else if (mustExist) {
    throw(sprintf("Failed to located Picard tools"))
  }

  verbose && exit(verbose)

  path
} # findPicard()