chipster.tools.path = '/opt/chipster/tools'
chipster.common.path = '/opt/chipster/comp/modules/common/R-2.12'
chipster.module.path = '/opt/chipster/comp/modules/ngs'
setwd("ca118dd1-8acf-475e-be0f-6c2231675374")
# TOOL bed-sort.R: "Sort BED" (Sorts a BED file by chromosome and then by start position. This tool is based on the BEDTools package.)
# INPUT regions.bed TYPE GENERIC 
# OUTPUT sorted.bed 



# EK 22.6.2011

# binary
binary <- c(file.path(chipster.tools.path, "bedtools", "bin", "sortBed"))

# command
command <- paste(binary, "-i regions.bed > sorted.bed")

# run
system(command)


print("script-finished-succesfully")
