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()
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