dbFinder/run-all.sh at master · LieberInstitute/dbFinder · GitHub

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#!/bin/sh

## Usage
# sh run-all.sh shulha run8-v1.5.35 TRUE
# sh run-all.sh epimap run1-v1.5.38 TRUE H3K27ac
# sh run-all.sh epimap run1-v1.5.38 TRUE H3K4me3

# Define variables
EXPERIMENT=$1
PREFIX=$2
SKIP1=${3-"FALSE"}
HISTONE=$4

mkdir -p ${EXPERIMENT}/CoverageInfo
mkdir -p ${EXPERIMENT}/derAnalysis
#mkdir -p ${EXPERIMENT}/regionMatrix
#mkdir -p ${EXPERIMENT}/regionMatrix-vs-DERs
#mkdir -p ${EXPERIMENT}/coverageToExon

if [[ $SKIP1 == "FALSE" ]]
then
    sh step1-fullCoverage.sh ${EXPERIMENT}
fi
sh step2-makeModels.sh ${EXPERIMENT} ${PREFIX} ${HISTONE}
sh step3-analyzeChr.sh ${EXPERIMENT} ${PREFIX} ${HISTONE}
sh step4-mergeResults.sh ${EXPERIMENT} ${PREFIX} ${HISTONE}
sh step5-derfinderReport.sh ${EXPERIMENT} ${PREFIX} ${HISTONE}

#if [[ $SKIP6 == "FALSE" ]]
#then
#    sh step6-regionMatrix.sh ${EXPERIMENT}
#fi
#sh step7-regMatVsDERs.sh ${EXPERIMENT} ${PREFIX}

#if [[ $SKIP8 == "FALSE" ]]
#then
#    sh step8-coverageToExon.sh ${EXPERIMENT}
#fi

#sh step9-summaryInfo.sh ${EXPERIMENT} ${PREFIX}