#!/bin/bash
# Multiple Runs of BioNetGen
# Modifications by Rafael J. Rodriguez

if [ "$1" = "-h" ]; then
     echo "Script to generate multiple runs of BioNetGen"
     echo "Usage: MultBNGSim full_path_to_vars.sh "
     echo "Example ~/Desktop/vars.sh"
     exit 0
elif [ "$1" = "-help" ]; then
     echo "Script to generate multiple runs of BioNetGen"
     echo "Usage: MultBNGSim full_path_to_vars.sh "
     echo "Example ~/Desktop/vars.sh"
     exit 0
elif [ "$1" = "" ]; then
     echo "Undefined parameters"
     echo "Usage: MultBNGSim full_path_to_vars.sh "
     echo "Example ~/Desktop/vars.sh"
     exit 1
fi
varsPath=$1

source $varsPath

outDir=$outputPath$label$(date +"%Y-%m-%d-%H-%M-%S")
mkdir $outDir
logfile="$name$(date +"%Y-%m-%d-%H-%M-%S").log"
touch $outDir/$logfile
curr_dir=$(pwd)

newDir="Run0"
mkdir $outDir/$newDir
echo "************************ Multiple Runs - Run 0 *******************" >> $outDir/$logfile
cd $outDir/$newDir
perl $scriptPath$script1 $model >> $outDir/$logfile
echo $scriptPath
echo $script1
echo $outDir
echo $logfile
cp ./*_write.net $curr_dir
cd $curr_dir
echo "Run number 0 complete"

for ((x=1; x < $runNumber ; x++))
do
   newDir="Run$x"
   mkdir $outDir/$newDir

   echo "************************ Multiple Runs - Run $x *******************" >> $outDir/$logfile
 
   cd $outDir/$newDir
   cp $curr_dir/*_write.net .
   perl $scriptPath$script2 $actions >> $outDir/$logfile

   cd $curr_dir
   echo "Run number $x complete"
done
touch $outDir/ssa
cp $model $outDir
cd $outDir
for f in `ls Run*/*_ssa.gdat`; do
	awk -f $awkFile $f >> ssa;
done;
find . -name *.cdat  -exec rm -rf {} \;
cd ..
echo "BioNetGen output available at $outDir/$logfile"