setup file for installing required packages for the comparison tools

diff --git a/tools/setup.R b/tools/setup.R
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--- /dev/null
+++ b/tools/setup.R
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+#!/usr/bin/Rscript
+
+###
+# Script and Functions for seting up required R-packages for RACS comparison tools
+###
+
+# define dependencies, ie. needed to be installed for the code to run
+# first packages that can be installaed from CRAN using install.packages()
+pckges <- c("xlsx","plotly")
+
+##############################################################################################
+# functions for checking whether dependencies are installed and install all needed packages
+
+
+# function to install neeeded packages
+NeededPackages <- function(pckges, otherPckgs="", def.mirror='https://cloud.r-project.org') {
+	RverM <- as.numeric(R.Version()['major'])
+	Rverm <- as.numeric(R.Version()['minor'])
+
+        availablePckges <- .packages(all.available = TRUE)
+
+	# deal with packages from CRAN
+        needTOinstall <- !(pckges %in% availablePckges)
+	if (sum(needTOinstall) == 0) {
+	    cat("Requested packages:")
+	    print(pckges)
+	    cat("installing...", pckges[needTOinstall], '\n')
+	    for (pck in pckges[needTOinstall]) {
+                install.packages(pck,repos=def.mirror)
+	    }
+	}
+
+	# deal with packages from BioConductor
+        needTOinstall <- !(otherPckgs %in% availablePckges)
+	if (sum(needTOinstall) == 0 ) {
+	    cat("Requested packages:")
+	    print(otherPckgs)
+	    cat("installing...", otherPckgs[needTOinstall], '\n')
+            for (pck in otherPckgs[needTOinstall]) {
+		print(RverM); print(Rverm)
+		if ((RverM >= 3 ) && (Rverm > 5)) {
+			# newer R version
+                        install.packages("BiocManager", repos=def.mirror)
+                        BiocManager::install(pck)
+		} else {
+			# older R versions...
+			source("https://bioconductor.org/biocLite.R")
+			library(BiocInstaller)
+			BiocInstaller::biocLite(pck)
+		}
+            }
+	}
+}
+
+# function to check the versions of a given set of packages...
+checkVersion <- function(pckges) {
+
+        print(sessionInfo())
+
+	print(pckges)
+
+        for (pck in pckges){
+                cat(pck, as.character(packageVersion(pck)), '\n')
+        }
+
+}
+
+##############################################################################################
+
+
+
+# check and install required packages
+NeededPackages(pckges)
+
+# display versions of the installed/required packages
+checkVersion(pckges)
+