naming to be more consistent

HICCUPS`

        dependhiccups="afterok:$jid"

	jid=`sbatch <<- ARROWS | egrep -o -e "\b[0-9]+$"

	jid=`sbatch <<- ARROWHEAD | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH -p $queue

	#SBATCH --mem-per-cpu=2G

	${sbatch_wait}

	${load_java}

	date

	${juiceDir}/scripts/juicer_arrows.sh -j ${juiceDir}/scripts/juicebox -i $outputdir/inter_30.hic

	${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicebox -i $outputdir/inter_30.hic

	date

ARROWS`

ARROWHEAD`

        dependarrows="${dependhiccups}:$jid"

	jid=`sbatch <<- FINCLN1 | egrep -o -e "\b[0-9]+$"

#!/bin/bash

##########

#The MIT License (MIT)

#

# Copyright (c) 2015 Aiden Lab

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal

# in the Software without restriction, including without limitation the rights

# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

# copies of the Software, and to permit persons to whom the Software is

# furnished to do so, subject to the following conditions:

#

# The above copyright notice and this permission notice shall be included in

# all copies or substantial portions of the Software.

#

#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

#  THE SOFTWARE.

##########

# Juicer postprocessing script.

# This will find contact domains with Arrowhead.

#Juicer 1.5

## Read arguments

usageHelp="Usage: ${0} [-h] -j <juicebox_file_path> -i <hic_file_path>"

printHelpAndExit() {

    echo "$usageHelp"

    exit $1

}

#set defaults

genomeID="hg19"

hic_file_path="$(pwd)/aligned/inter_30.hic"

juiceboxpath="/broad/aidenlab/scripts/juicebox"

while getopts "h:j:i:" opt; do

    case $opt in

	h) printHelpAndExit 0;;

	j) juiceboxpath=$OPTARG ;;

	i) hic_file_path=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done

## Check that juicebox exists 

if [ ! -e "${juiceboxpath}" ]; then

  echo "***! Can't find juicebox in ${juiceboxpath}";

  exit 100;

fi

## Check that hic file exists    

if [ ! -e "${hic_file_path}" ]; then

  echo "***! Can't find inter.hic in ${hic_file_path}";

  exit 100;

fi

echo -e "${juiceboxpath} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"

echo -e "ARROWHEAD:\n"

${juiceboxpath} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"

if [ $? -ne 0 ]; then

    echo "***! Problem while running Arrowhead";

    exit 100

else

    echo -e "\n(-: Arrowhead Postprocessing successfully completed (-:"

fi

#!/bin/bash

##########

#The MIT License (MIT)

#

# Copyright (c) 2015 Aiden Lab

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal

# in the Software without restriction, including without limitation the rights

# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

# copies of the Software, and to permit persons to whom the Software is

# furnished to do so, subject to the following conditions:

#

# The above copyright notice and this permission notice shall be included in

# all copies or substantial portions of the Software.

#

#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

#  THE SOFTWARE.

##########

# Juicer postprocessing script.

# This will run the major post-processing on the HiC file, including finding

# loops with HiCCUPS and inding motifs of these loops with MotifFinder.

# Juicer 1.5

## Read arguments

usageHelp="Usage: ${0} [-h] -j <juicebox_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>"

printHelpAndExit() {

    echo "$usageHelp"

    exit $1

}

#set defaults

genomeID="hg19"

hic_file_path="$(pwd)/aligned/inter_30.hic"

juiceboxpath="/broad/aidenlab/scripts/juicebox"

bed_file_dir="/broad/aidenlab/references/motif"

while getopts "h:g:j:i:m:" opt; do

    case $opt in

	h) printHelpAndExit 0;;

	j) juiceboxpath=$OPTARG ;;

	i) hic_file_path=$OPTARG ;;

	m) bed_file_dir=$OPTARG ;; 

	g) genomeID=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done

## Check that juicebox exists 

if [ ! -e "${juiceboxpath}" ]; then

  echo "***! Can't find juicebox in ${juiceboxpath}";

  exit 100;

fi

## Check that hic file exists    

if [ ! -e "${hic_file_path}" ]; then

  echo "***! Can't find inter.hic in ${hic_file_path}";

  exit 100;

fi

## Check that bed folder exists    

if [ ! -e "${bed_file_dir}" ]; then

  echo "***! Can't find folder ${bed_file_dir}";

  exit 100;

fi

echo -e "\nHiCCUPS:\n"

${juiceboxpath} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"

if [ $? -ne 0 ]; then

    echo "***! Problem while running HiCCUPS";

    exit 100

fi

if [ -f ${hic_file_path%.*}"_loops.txt" ]

then

    echo -e "\nAPA:\n"

    ${juiceboxpath} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"

    echo -e "\nMOTIF FINDER:\n"

    ${juiceboxpath} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"

    echo -e "\n(-: Feature annotation successfully completed (-:"

else

    # if loop lists do not exist but Juicebox didn't return an error, likely 

    # too sparse

    echo -e "\n(-: Postprocessing successfully completed, maps too sparse to annotate (-:"

fi