#!/bin/bash

###########################################
# The CCseqBasic installation is located here :
pipePath="/t1-home/molhaem2/telenius/CCseqBasic/CS5/"
###########################################

# This is the genome build for the run :

Genome="hg19"


# capturesiteFile is the RE fragment coordinate input file (containing the dpnII fragments within which your biotinylated capture oligos are) :
# Make this file with this tutorial : http://userweb.molbiol.ox.ac.uk/public/telenius/CaptureCompendium/CCseqBasic/3_run/fragmentfile.html

capturesiteFile="/t1-data/user/telenius/CCseqBasicFragmentFile.txt"


#############################################
# We are now here (the current directory) - the directory we are now running the pipe :

rundir=$( pwd )


# Tell where we are - print it to output :

echo "Running CCseqBasic5.sh in folder ${rundir}"


# Tell the command to user - print it to output :

echo "${pipePath}/CCseqBasic5.sh -c "${capturesiteFile}" --genome ${Genome} --onlyBlat"


# Run the command :

${pipePath}/CCseqBasic5.sh -c "${capturesiteFile}" --genome ${Genome} --onlyBlat



# Tell the user that we are now finished :

echo "All done !"