FitHiChIP_Docker.sh

#!/bin/bash

usage(){
cat << EOF
Options:
   	-C  ConfigFile		Name of the configuration file storing the parameters of FitHiChIP.
EOF
}

while getopts "C:" opt;
do
	case "$opt" in
		C) ConfigFile=$OPTARG;;
		\?) usage
			echo "error: unrecognized option -$OPTARG";
			exit 1
			;;
	esac
done

#======================
# default values of the parameters
#======================

# input files
# 3 different ways to provide input to FitHiChIP
# option 1: provide a valid pairs file generated from HiC pro pipeline
InpValidPairsFile=""
# option 2: provide the bin intervakl file and the matrix file generated from HiC pro pipeline
InpBinIntervalFile=""
InpMatrixFile=""
# option 3: provide the set of locus pairs 
# (6 columns storing the interacting bins and the 7th column storing the contact count)
InpInitialInteractionBedFile=""
# reference ChIP-seq / HiChIP peak file
PeakFILE=""
# prefix string used for every output file
PREFIX='FitHiChIP'
# size of the chromosome that is to be provided
ChrSizeFile=""
# reference chromosome fasta file
RefFastaFile=""
# reference chromosome based mappability file
# (may be downloaded from the site  http://hgdownload.cse.ucsc.edu/goldenPath/)
MappabilityFile=""
# restriction fragment file compatible with the reference chromosome
REFragFile=""
# window size used to compute GC content
GCContentWindowSize=200
# window size used to compute the mappability
MappabilityWindowSize=500
# 5 Kb resolution
BIN_SIZE=5000
# FDR threshold
QVALUE=0.01
# default value of output directory is the present working directory
OutDir=`pwd`'/'
# lower distance threshold for two cis interactions
LowDistThres=20000	# 20 Kb
# upper distance threshold for two cis interactions
UppDistThres=2000000 # 2 Mb
# number of bins employed for FitHiChIP
NBins=200
# default value of plotting analysis figures
DrawFig=0
# option to note down the timing information
TimeProf=0
# boolean variable indicating that previous existing output files
# will be overwritten (1) or not (0 - default)
OverWrite=0

#=========================
# Significant interaction call 
# and the bias correction related parameters
#=========================
# denotes the type of Interaction
# 1: peak to peak, 2: peak to non peak
# 3: peak to all (default) 4: all to all
# 5: accounting for all of 1 to 4
IntType=3
# variable indicating bias correction (1: On, 0: off)
# recommended = 1
BiasCorr=1
# type of bias vector (if bias correction is employed)
# 1: coverage specific bias
# 2: ICE specific bias (default)
BiasType=1
# temporary variable (binary)
# used to model FitHiChIP peak to all interactions
# using peak to peak background only
# applicable for only peak to all interactions
UseP2PBackgrnd=1
# Merging interactions which are near to each other
MergeInteraction=1
# if the reference genome is circular genome
CircularGenome=0

#========================
# following parameters are now obsolete
# so keeping them in a default state
# user cannot alter these values
#========================
# default lower cutoff of bias value
biaslowthr=0.2
# default higher cutoff of bias value
biashighthr=5
# boolean variable for pre-filtering the interactions according to the bias value
BeginBiasFilter=0
# boolean variable for probability adjustment of the interactions according to the bias value
EndBiasFilter=0
# temporary variable (binary)
# if 1, includes only nonzero contact based locus pairs for
# FitHiC spline fit implementation
# default : 0
UseNonzeroContacts=0
# two variables used for bias correction
# modeling the regression between observed contact count
# and the bias variables
resid_biascorr=0
eqocc_biascorr=1
# boolean variable indicating whether for bias correction
# multiplicative bias value would be used
# defult 0
MultBias=0
#========================

#==============================
# read the configuration file and store various parameters
#==============================


# separator used in the config file
IFS="="
while read -r name value
do
	param=$name
	paramval=${value//\"/}
	if [[ -n $param ]]; then
		if [[ $param != \#* ]]; then
			# if there are multiple parameter values (separated by # - old values are kept)
			# then the following operation selects the current one
			paramval=$(echo "$paramval" | awk -F['#\t'] '{print $1}' | tr -d '[:space:]');
			if [ $param == "ValidPairs" ]; then
				InpValidPairsFile=$paramval
			fi
			if [ $param == "Interval" ]; then
				InpBinIntervalFile=$paramval
			fi
			if [ $param == "Matrix" ]; then
				InpMatrixFile=$paramval
			fi
			if [ $param == "Bed" ]; then
				InpInitialInteractionBedFile=$paramval
			fi
			if [ $param == "HIC" ]; then
				InpHiCFile=$paramval
			fi
			if [ $param == "COOL" ]; then
				InpCoolFile=$paramval
			fi									
			## indicates circular genome
			if [ $param == "CircularGenome" ]; then
				CircularGenome=$paramval
			fi			
			if [ $param == "PeakFile" ]; then
				PeakFILE=$paramval
			fi
			if [ $param == "OutDir" ]; then
				if [[ ! -z $paramval ]]; then
					OutDir=$paramval
				fi
			fi
			if [ $param == "ChrSizeFile" ]; then
				ChrSizeFile=$paramval
			fi

			# optional parameters
			if [ $param == "MappabilityFile" ]; then
				MappabilityFile=$paramval
			fi
			if [ $param == "RefFasta" ]; then
				RefFastaFile=$paramval
			fi
			if [ $param == "REFragFile" ]; then
				REFragFile=$paramval
			fi
			if [ $param == "GCSize" ]; then
				if [[ ! -z $paramval ]]; then
					GCContentWindowSize=$paramval
				fi
			fi
			if [ $param == "MappSize" ]; then
				if [[ ! -z $paramval ]]; then
					MappabilityWindowSize=$paramval
				fi
			fi
			# end optional parameters

			if [ $param == "BINSIZE" ]; then
				if [[ ! -z $paramval ]]; then
					BIN_SIZE=$paramval
				fi
			fi
			if [ $param == "LowDistThr" ]; then
				if [[ ! -z $paramval ]]; then
					LowDistThres=$paramval
				fi
			fi
			if [ $param == "UppDistThr" ]; then
				if [[ ! -z $paramval ]]; then
					UppDistThres=$paramval
				fi
			fi
			if [ $param == "QVALUE" ]; then
				if [[ ! -z $paramval ]]; then
					QVALUE=$paramval
				fi
			fi
			if [ $param == "NBins" ]; then
				if [[ ! -z $paramval ]]; then
					NBins=$paramval
				fi
			fi
			if [ $param == "PREFIX" ]; then
				if [[ ! -z $paramval ]]; then
					PREFIX=$paramval
				fi
			fi
			if [ $param == "Draw" ]; then
				if [[ ! -z $paramval ]]; then
					DrawFig=$paramval
				fi
			fi
			if [ $param == "TimeProf" ]; then
				if [[ ! -z $paramval ]]; then
					TimeProf=$paramval
				fi
			fi

			# these parameters are not required for the moment
			# if [ $param == "BeginBiasFilter" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		BeginBiasFilter=$paramval
			# 	fi
			# fi
			# if [ $param == "EndBiasFilter" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		EndBiasFilter=$paramval
			# 	fi
			# fi
			# if [ $param == "biaslowthr" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		biaslowthr=$paramval
			# 	fi
			# fi			
			# if [ $param == "biashighthr" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		biashighthr=$paramval
			# 	fi
			# fi
			# if [ $param == "MultBias" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		MultBias=$paramval
			# 	fi
			# fi	
			# if [ $param == "BiasCorrResid" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		resid_biascorr=$paramval
			# 	fi
			# fi	
			# if [ $param == "BiasCorrEqOcc" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		eqocc_biascorr=$paramval
			# 	fi
			# fi	
			# if [ $param == "UseNonzeroContacts" ]; then
			# 	if [[ ! -z $paramval ]]; then
			# 		UseNonzeroContacts=$paramval
			# 	fi
			# fi			
			# end non-required parameters

			if [ $param == "MergeInt" ]; then
				if [[ ! -z $paramval ]]; then
					MergeInteraction=$paramval
				fi
			fi

			# these four variables are added - sourya
			if [ $param == "BiasType" ]; then
				if [[ ! -z $paramval ]]; then
					BiasType=$paramval
				fi
			fi
			if [ $param == "UseP2PBackgrnd" ]; then
				if [[ ! -z $paramval ]]; then
					UseP2PBackgrnd=$paramval
				fi
			fi			
			if [ $param == "OverWrite" ]; then
				if [[ ! -z $paramval ]]; then
					OverWrite=$paramval
				fi
			fi
			if [ $param == "IntType" ]; then
				if [[ ! -z $paramval ]]; then
					IntType=$paramval
				fi
			fi
			if [ $param == "BiasCorrection" ]; then
				if [[ ! -z $paramval ]]; then
					BiasCorr=$paramval
				fi
			fi
			# end add - sourya

		fi
	fi
done < $ConfigFile

#===================
# verify the input parameters
#===================
echo -e "\n ================ Verifying input configuration parameters ================="

if [[ -z $InpValidPairsFile && -z $InpInitialInteractionBedFile && -z $InpHiCFile && -z $InpCoolFile ]]; then
	if [[ -z $InpBinIntervalFile || -z $InpMatrixFile ]]; then
		echo -e 'There are five ways to provide FitHiChIP input: \n 1) provide valid pairs file (from HiC pro pipeline), \n 2) Provide both bin interval and matrix files (from HiC pro pipeline), \n 3) provide a file in the Bed= option - either as a set of locus pairs along with their contact counts (7 columns), 4) Provide interactions in .hic format (from Juicer), or 5) Provide interactions in .cool format. \n But user did not provide any of these input configurations. - exit !!'
		exit 1
	fi
fi

if [[ -z $PeakFILE ]]; then
	if [[ $IntType != 4 ]]; then
		echo 'Input interaction type specified requires peak file information - but no reference peak file (either ChIP or HiChIP) is provided - exit !!'
		exit 1
	fi
fi

#======================
# these parameters are not mandatory 
# so warning messages are removed

# if [[ -z $RefFastaFile ]]; then
# 	echo 'User should provide reference chromosome fasta file - quit !!'
# 	exit 1
# fi

# if [[ -z $REFragFile ]]; then
# 	echo 'User should provide a restriction fragment file - quit !!'
# 	exit 1
# fi

# if [[ -z $MappabilityFile ]]; then
# 	echo 'Reference mappability file is not specified - exit !!'
# 	exit 1
# fi
#======================

if [[ -z $ChrSizeFile ]]; then
	echo 'ERROR ====>>> Chromosome size file is not specified - exit !!'
	exit 1
fi

echo '***** Specified output directory : '$OutDir

# boolean variable indicating error condition
errcond=0

##=============
## if Bed file / HiC file / cool file is not provided, 
## means we need to process the valid pairs
## and there is no matrix file or bin interval file
## then, get the installed HiC-pro version
##=============
HiCProExec=`which HiC-Pro`
if [[ -z $HiCProExec ]]; then
	echo 'ERROR ===>>>> HiC-pro is not installed in the system - FitHiChIP quits !!!'
	exit 1
fi
# path of HiC pro executable
# of the format somedir/bin/HiC-Pro		
d1=$(dirname ${HiCProExec})
HiCProBasedir=$(dirname ${d1})
echo 'Base directory containing HiCPro package : '$HiCProBasedir
if [[ -z $HiCProBasedir ]]; then
	echo 'ERROR ====>>> Invalid HiC-pro installation directory - FitHiChIP quits - exit !!'
	exit 1
fi

#*****************************
# error checking - 
# check if the required libraries are all installed or not
#*****************************

## first check the python version
# note: FitHiChIP new versions now use python3, instead of python2
# check if python3 is installed and its version is > 3.4
pythonversion=$(python3 --version 2>&1 | head -n 1 | awk '{print $2}' -)
if [[ -z "$pythonversion" ]]; then
    echo "ERROR ====>>> No Python installation is detected in the system !!! FitHiChIP quits !!!" 
    errcond=1
fi
numfield=`echo $pythonversion | awk -F'[.]' '{print NF}' -`
if [[ $numfield -ge 3 ]]; then
	num1=`echo $pythonversion | awk -F'[.]' '{print $1}' -`
	num2=`echo $pythonversion | awk -F'[.]' '{print $2}' -`
	num3=`echo $pythonversion | awk -F'[.]' '{print $3}' -`
	if [[ $num1 -gt 3 ]]; then
		echo "Installed python version: "${pythonversion}
	elif [[ $num1 -eq 3 && $num2 -gt 4 ]]; then
		echo "Installed python version: "${pythonversion}
	elif [[ $num1 -eq 3 && $num2 -eq 4 && $num3 -ge 1 ]]; then
		echo "Installed python version: "${pythonversion}
	else 
		echo " --- FitHiChIP now works on python 3 - should be python3 with version >= 3.4 !!! FitHiChIP quits !!!"
		errcond=1
	fi
else
	num1=`echo $pythonversion | awk -F'[.]' '{print $1}' -`
	num2=`echo $pythonversion | awk -F'[.]' '{print $2}' -`
	if [[ $num1 -gt 3 ]]; then
		echo "Installed python version: "${pythonversion}
	elif [[ $num1 -eq 3 && $num2 -gt 3 ]]; then
		echo "Installed python version: "${pythonversion}
	else 
		echo " --- FitHiChIP now works on python 3 - should be python3 with version >= 3.4 !!! FitHiChIP quits !!!"
		errcond=1
	fi	
fi

# check if python3 libraries are also installed
if python3 -c "import gzip"; then
    echo '*** Python library gzip is installed'
else
    echo 'ERROR ====>>> Python3 library gzip is not installed !!! FitHiChIP quits !!!'
    errcond=1
fi
if python3 -c "from optparse import OptionParser"; then
    echo '*** Python module OptionParser (from the package optparse) is installed'
else
    echo 'ERROR ====>>> Python module OptionParser (from the package optparse) is not installed !!! FitHiChIP quits !!!'
    errcond=1
fi
if python3 -c "import networkx"; then
    echo '*** Python package networkx is installed'
else
    echo 'ERROR ====>>> Python3 package networkx is not installed !!! Try to install the package by python3 -m pip install networkx. FitHiChIP quits !!!'
    errcond=1
fi

# check if MACS2 package is installed
macs2version=$(macs2 --version 2>&1 |  head -n 1 | awk -F[" "] '{print $2 }' -)
if [[ -z "$macs2version" ]]; then
    echo "ERROR ====>>> MACS2 peak calling package is not detected in the system !!! Try to install the package by python3 -m pip install MACS2. FitHiChIP quits !!!" 
    errcond=1
else
	echo "*** Found MACS2 package (for peak calling) installed in the system -  "$macs2version
fi

# check the R version
Rversion=$(R --version | head -n 1 | awk -F[" "] '{print $3}' -)
if [[ -z "$Rversion" ]]; then
    echo "ERROR ====>>> No R installation is detected in the system !!! FitHiChIP quits !!!" 
    errcond=1
fi
numfield=`echo $Rversion | awk -F'[.]' '{print NF}' -`
if [[ $numfield -ge 3 ]]; then
	num1=`echo $Rversion | awk -F'[.]' '{print $1}' -`
	num2=`echo $Rversion | awk -F'[.]' '{print $2}' -`
	num3=`echo $Rversion | awk -F'[.]' '{print $3}' -`
	if [[ $num1 -gt 3 ]]; then
		echo "Installed R version: "${Rversion}
	elif [[ $num1 -eq 3 && $num2 -gt 3 ]]; then
		echo "Installed R version: "${Rversion}
	elif [[ $num1 -eq 3 && $num2 -eq 3 && $num3 -ge 0 ]]; then
		echo "Installed R version: "${Rversion}
	else 
		echo " -- R version should be at least R 3.3 !!! FitHiChIP quits !!!"
		errcond=1
	fi
else
	num1=`echo $Rversion | awk -F'[.]' '{print $1}' -`
	num2=`echo $Rversion | awk -F'[.]' '{print $2}' -`
	if [[ $num1 -gt 3 ]]; then
		echo "Installed R version: "${Rversion}
	elif [[ $num1 -eq 3 && $num2 -gt 3 ]]; then
		echo "Installed R version: "${Rversion}
	else 
		echo " -- R version should be at least R 3.3 !!! FitHiChIP quits !!!"
		errcond=1
	fi	
fi

# check the samtools version
samtoolsversion=$(samtools 2>&1 | grep "Version" | awk -F[" "] '{print $2}' -)
if [[ -z "$samtoolsversion" ]]; then
    echo "ERROR ====>>> No samtools installation is detected in the system !!! FitHiChIP quits !!!" 
    errcond=1
    # exit 1
fi
numfield=`echo $samtoolsversion | awk -F'[.]' '{print NF}' -`
if [[ $numfield -ge 3 ]]; then
	num1=`echo $samtoolsversion | awk -F'[.]' '{print $1}' -`
	num2=`echo $samtoolsversion | awk -F'[.]' '{print $2}' -`
	num3=`echo $samtoolsversion | awk -F'[.]' '{print $3}' -`
	if [[ $num1 -gt 1 ]]; then
		echo "Installed samtools version: "${samtoolsversion}
	elif [[ $num1 -eq 1 && $num2 -gt 6 ]]; then
		echo "Installed samtools version: "${samtoolsversion}
	elif [[ $num1 -eq 1 && $num2 -eq 6 && $num3 -ge 0 ]]; then
		echo "Installed samtools version: "${samtoolsversion}
	else 
		echo " - Samtools version should be at least 1.6 !!! FitHiChIP quits !!!"
		errcond=1
	fi
else
	num1=`echo $samtoolsversion | awk -F'[.]' '{print $1}' -`
	num2=`echo $samtoolsversion | awk -F'[.]' '{print $2}' -`
	if [[ $num1 -gt 1 ]]; then
		echo "Installed samtools version: "${samtoolsversion}
	elif [[ $num1 -eq 1 && $num2 -gt 6 ]]; then
		echo "Installed samtools version: "${samtoolsversion}
	else 
		echo " - Samtools version should be at least 1.6 !!! FitHiChIP quits !!!"
		errcond=1
	fi	
fi

# check if bgzip is installed in the system
bgzipnum=`bgzip -h 2>&1 | wc -l`
if [[ $bgzipnum -gt 5 ]]; then
	echo "*** bgzip utility is installed in the system"
else
	echo "ERROR =====>> bgzip utility is NOT installed in the system -- please install it from htslib (associated with samtools) version >= 1.6"
	errcond=1
fi

# check if tabix is installed in the system
tabixnum=`tabix -h 2>&1 | wc -l`
if [[ $tabixnum -gt 5 ]]; then
	echo "*** tabix utility is installed in the system"
else
	echo "ERROR =====>> tabix utility is NOT installed in the system -- please install it from htslib (associated with samtools) version >= 1.6"
	errcond=1
fi

# check the bedtools version
# command 1
bedtoolsversion1=$(bedtools --version | head -n 1 | awk -F[" "] '{print substr($2,2); }' -)
# echo "bedtoolsversion1: "$bedtoolsversion1
# command 2
bedtoolsversion2=$(bedtools 2>&1 | grep "Version" | awk -F[" "] '{print substr($NF,2); }' -)
# echo "bedtoolsversion2: "$bedtoolsversion2
# if both commands fail then surely bedtools is not installed in the system
if [[ -z "$bedtoolsversion1" && -z "$bedtoolsversion2" ]]; then
    echo "ERROR ====>>> No bedtools installation is detected in the system !!! FitHiChIP quits !!!" 
    errcond=1
fi
if [[ ! -z "$bedtoolsversion1" ]]; then

	numfield=`echo $bedtoolsversion1 | awk -F'[.]' '{print NF}' -`
	if [[ $numfield -ge 3 ]]; then
		num1=`echo $bedtoolsversion1 | awk -F'[.]' '{print $1}' -`
		num2=`echo $bedtoolsversion1 | awk -F'[.]' '{print $2}' -`
		num3=`echo $bedtoolsversion1 | awk -F'[.]' '{print $3}' -`
		if [[ $num1 -gt 2 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion1}
		elif [[ $num1 -eq 2 && $num2 -gt 26 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion1}
		elif [[ $num1 -eq 2 && $num2 -eq 26 && $num3 -ge 0 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion1}
		else 
			echo " - bedtools version should be at least 2.26.0 !!! FitHiChIP quits !!!"
			errcond=1
		fi
	else
		num1=`echo $bedtoolsversion1 | awk -F'[.]' '{print $1}' -`
		num2=`echo $bedtoolsversion1 | awk -F'[.]' '{print $2}' -`
		if [[ $num1 -gt 2 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion1}
		elif [[ $num1 -eq 2 && $num2 -gt 26 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion1}
		else 
			echo " - bedtools version should be at least 2.26.0 !!! FitHiChIP quits !!!"
			errcond=1
		fi	
	fi
fi

if [[ -z "$bedtoolsversion1" && ! -z "$bedtoolsversion2" ]]; then
    
	numfield=`echo $bedtoolsversion2 | awk -F'[.]' '{print NF}' -`
	if [[ $numfield -ge 3 ]]; then
		num1=`echo $bedtoolsversion2 | awk -F'[.]' '{print $1}' -`
		num2=`echo $bedtoolsversion2 | awk -F'[.]' '{print $2}' -`
		num3=`echo $bedtoolsversion2 | awk -F'[.]' '{print $3}' -`
		if [[ $num1 -gt 2 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion2}
		elif [[ $num1 -eq 2 && $num2 -gt 26 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion2}
		elif [[ $num1 -eq 2 && $num2 -eq 26 && $num3 -ge 0 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion2}
		else 
			echo " - bedtools version should be at least 2.26.0 !!! FitHiChIP quits !!!"
			errcond=1
		fi
	else
		num1=`echo $bedtoolsversion2 | awk -F'[.]' '{print $1}' -`
		num2=`echo $bedtoolsversion2 | awk -F'[.]' '{print $2}' -`
		if [[ $num1 -gt 2 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion2}
		elif [[ $num1 -eq 2 && $num2 -gt 26 ]]; then
			echo "Installed bedtools version: "${bedtoolsversion2}
		else 
			echo " - bedtools version should be at least 2.26.0 !!! FitHiChIP quits !!!"
			errcond=1
		fi	
	fi
fi

# final evaluation
if [[ $errcond == 1 ]]; then
	echo " --------->>>>>> ERROR - current system has one or more packages missing" 
	echo " ------- please check the above logs and install the missing packages before executing FitHiChIP"
	echo " ------- exiting for the moment !!"
	exit 1
fi

#*****************************
# here check if the configuration file has relative path names as the input
# in such a case, convert the relative path names (with respect to the location of the configuration file itself)
# in the absolute file
# also perform Error checking - check if input files provided are correct
# i.e. these files exist

echo -e "\n\n ====== Changing relative pathnames of the input files to their absolute path names ========== \n\n"

# directory of the configuration file
ConfigFileDir="$(cd $(dirname $ConfigFile); pwd)"
BINDARG=("-v$ConfigFileDir:$ConfigFileDir")
#BINDARG+=("-v$TMPDIR:$TMPDIR")

# first go to the configuration file directory
cd $ConfigFileDir

if [[ ! -z $InpValidPairsFile ]]; then
	if [ ! -f $InpValidPairsFile ]; then
		echo 'ERROR ===>>>> Valid pairs file provided as input : '$InpValidPairsFile
		echo 'However, no such valid pairs file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${InpValidPairsFile:0:1}" != / && "${InpValidPairsFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		InpValidPairsFile="$(cd $(dirname $InpValidPairsFile); pwd)/$(basename $InpValidPairsFile)"
	fi
	BINDARG+=("-v$(dirname $InpValidPairsFile):$(dirname $InpValidPairsFile)")
fi

if [[ ! -z $InpBinIntervalFile ]]; then
	if [ ! -f $InpBinIntervalFile ]; then
		echo 'ERROR ===>>>> Bin interval file provided as input : '$InpBinIntervalFile
		echo 'However, no such bin interval file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${InpBinIntervalFile:0:1}" != / && "${InpBinIntervalFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		InpBinIntervalFile="$(cd $(dirname $InpBinIntervalFile); pwd)/$(basename $InpBinIntervalFile)"
	fi
	BINDARG+=("-v$(dirname $InpBinIntervalFile):$(dirname $InpBinIntervalFile)")
fi

if [[ ! -z $InpMatrixFile ]]; then
	if [ ! -f $InpMatrixFile ]; then
		echo 'ERROR ===>>>> HiChIP matrix file provided as input : '$InpMatrixFile
		echo 'However, no such matrix file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi	
	if [[ "${InpMatrixFile:0:1}" != / && "${InpMatrixFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		InpMatrixFile="$(cd $(dirname $InpMatrixFile); pwd)/$(basename $InpMatrixFile)"
	fi
	BINDARG+=("-v$(dirname $InpMatrixFile):$(dirname $InpMatrixFile)")
fi

if [[ ! -z $InpInitialInteractionBedFile ]]; then
	if [ ! -f $InpInitialInteractionBedFile ]; then
		echo 'ERROR ===>>>> Pre-computed locus pairs (along with their contact counts) are provided as input : '$InpInitialInteractionBedFile
		echo 'However, no such file containing locus pairs exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi	
	if [[ "${InpInitialInteractionBedFile:0:1}" != / && "${InpInitialInteractionBedFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		InpInitialInteractionBedFile="$(cd $(dirname $InpInitialInteractionBedFile); pwd)/$(basename $InpInitialInteractionBedFile)"
	fi
	BINDARG+=("-v$(dirname $InpInitialInteractionBedFile):$(dirname $InpInitialInteractionBedFile)")
fi

if [[ ! -z $InpHiCFile ]]; then
	if [ ! -f $InpHiCFile ]; then
		echo 'ERROR ===>>>> .hic contact matrix file is provided as input : '$InpHiCFile
		echo 'However, no such file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi	
	if [[ "${InpHiCFile:0:1}" != / && "${InpHiCFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		InpHiCFile="$(cd $(dirname $InpHiCFile); pwd)/$(basename $InpHiCFile)"
	fi
	BINDARG+=("-v$(dirname $InpHiCFile):$(dirname $InpHiCFile)")
fi

if [[ ! -z $InpCoolFile ]]; then
	if [ ! -f $InpCoolFile ]; then
		echo 'ERROR ===>>>> .cool contact matrix file is provided as input : '$InpCoolFile
		echo 'However, no such file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi	
	if [[ "${InpCoolFile:0:1}" != / && "${InpCoolFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		InpCoolFile="$(cd $(dirname $InpCoolFile); pwd)/$(basename $InpCoolFile)"
	fi
	BINDARG+=("-v$(dirname $InpCoolFile):$(dirname $InpCoolFile)")
fi


if [[ ! -z $PeakFILE ]]; then
	if [ ! -f $PeakFILE ]; then
		echo 'ERROR ===>>>> Peak file provided as input : '$PeakFILE
		echo 'However, no such peak file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${PeakFILE:0:1}" != / && "${PeakFILE:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		PeakFILE="$(cd $(dirname $PeakFILE); pwd)/$(basename $PeakFILE)"
	fi
	BINDARG+=("-v$(dirname $PeakFILE):$(dirname $PeakFILE)")
fi

if [[ ! -z $RefFastaFile ]]; then
	if [ ! -f $RefFastaFile ]; then
		echo 'ERROR ===>>>> Fasta file of reference genome provided as input : '$RefFastaFile
		echo 'However, no such fasta file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${RefFastaFile:0:1}" != / && "${RefFastaFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		RefFastaFile="$(cd $(dirname $RefFastaFile); pwd)/$(basename $RefFastaFile)"
	fi
	BINDARG+=("-v$(dirname $RefFastaFile):$(dirname $RefFastaFile)")
fi

if [[ ! -z $REFragFile ]]; then
	if [ ! -f $REFragFile ]; then
		echo 'ERROR ===>>>> Restriction fragment file provided as input : '$REFragFile
		echo 'However, no such restriction fragment file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${REFragFile:0:1}" != / && "${REFragFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		REFragFile="$(cd $(dirname $REFragFile); pwd)/$(basename $REFragFile)"
	fi
	BINDARG+=("-v$(dirname $REFragFile):$(dirname $REFragFile)")
fi

if [[ ! -z $ChrSizeFile ]]; then
	if [ ! -f $ChrSizeFile ]; then
		echo 'ERROR ===>>>> File containing size of chromosomes for the reference genome, as provided : '$ChrSizeFile
		echo 'However, no such chromosome size containing file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${ChrSizeFile:0:1}" != / && "${ChrSizeFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		ChrSizeFile="$(cd $(dirname $ChrSizeFile); pwd)/$(basename $ChrSizeFile)"
	fi
	BINDARG+=("-v$(dirname $ChrSizeFile):$(dirname $ChrSizeFile)")
fi

if [[ ! -z $MappabilityFile ]]; then
	if [ ! -f $MappabilityFile ]; then
		echo 'ERROR ===>>>> Mappability information containing file provided as input : '$MappabilityFile
		echo 'However, no such Mappability related file exists - check input file and path - FitHiChIP quits !!'
		exit 1
	fi
	if [[ "${MappabilityFile:0:1}" != / && "${MappabilityFile:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		MappabilityFile="$(cd $(dirname $MappabilityFile); pwd)/$(basename $MappabilityFile)"
	fi
	BINDARG+=("-v$(dirname $MappabilityFile):$(dirname $MappabilityFile)")
fi

if [[ ! -z $OutDir ]]; then
	if [[ "${OutDir:0:1}" != / && "${OutDir:0:2}" != ~[/a-z] ]]; then
		# relative path - convert to absolute path
		OutDir="$(cd $(dirname $OutDir); pwd)/$(basename $OutDir)"
	fi
	BINDARG+=("-v$OutDir:$OutDir")
fi
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

#echo ${BINDARG[@]}
docker run "${BINDARG[@]}" --entrypoint /bin/bash aylab/fithichip /FitHiChIP/FitHiChIP_HiCPro.sh -C "$(cd $(dirname $ConfigFile); pwd)/$(basename $ConfigFile)" -s
#bash "$DIR/FitHiChIP_HiCPro.sh" -C "$ConfigFile" -s