R/findTopHat.R

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

findTopHat <- function(..., command="tophat", path=NULL) {
  if (is.null(path)) {
    # Aroma-specific variable
    path <- getExternalHome("TOPHAT_HOME")
  }
  versionPattern <- c("--version"=".*TopHat[ ]*v([0-9.-]+).*")
  findExternal(command=command, path=path, versionPattern=versionPattern, ...)
} # findTopHat()


findTopHat1 <- function(..., command="tophat", version=c(1,2)) {
  # Aroma-specific variable
  path <- getExternalHome("TOPHAT1_HOME")
  findTopHat(..., command=command, path=path, version=version)
} # findTopHat1()


findTopHat2 <- function(..., command="tophat2", version=c(2,3)) {
  # Aroma-specific variable
  path <- getExternalHome("TOPHAT2_HOME")
  res <- tryCatch({
    findTopHat(..., command=command, path=path, version=version)
  }, error = function(ex) { NULL })
  if (is.null(res)) {
    res <- findTopHat(..., command="tophat", version=version)
  }
  res
} # findTopHat2()