#!/bin/bash
# Multiple Runs of BioNetGen 2.1.8 (Not for 2.1.7!)

if [ "$1" = "-h" ]; then
     echo "Script to generate multiple runs of BioNetGen"
     echo "Usage: MultBNGSim full_path_to_BNG2.pl full_name_of_model_file output_path number_of_runs"
     echo "Example ~/Desktop/RuleBender/BioNetGen-2.1.7/Perl2/ ~/Desktop/Model.bngl ~/Desktop/workspace/ 5"
     exit 0
elif [ "$1" = "-help" ]; then
     echo "Script to generate multiple runs of BioNetGen"
     echo "Usage: MultBNGSim full_path_to_BNG2.pl full_name_of_model_file output_path number_of_runs"
     echo "Example ~/Desktop/RuleBender/BioNetGen-2.1.7/Perl2/ ~/Desktop/Model.bngl ~/Desktop/workspace/ 5"
     exit 0
elif [ "$1" = "" ]; then
     echo "Undefined parameters"
     echo "Usage: MultBNGSim full_path_to_BNG2.pl full_name_of_model_file output_path number_of_runs"
     echo "Example ~/Desktop/RuleBender/BioNetGen-2.1.7/Perl2/ ~/Desktop/Model.bngl ~/Desktop/workspace/ 5"
     exit 1
fi

scriptPath=$1
model=$2
outputPath=$3
runNumber=$4
script="BNG2.pl"

outDir=$outputPath$(date +"%Y-%m-%d-%H-%M-%S")

echo $outputPath
echo $outDir

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

for ((x=0; x < $runNumber ; x++))
do
   newDir="Run$x"
   mkdir $outDir/$newDir

   echo "************************ Multiple Runs - Run $x *******************" >> $outDir/$logfile
 
   cd $outDir/$newDir
   perl $scriptPath$script $model >> $outDir/$logfile

   cd $curr_dir
   #rm $outDir/$newDir/*.cdat   # may want to use this 
   echo "Run number $x complete"
done

echo "BioNetGen output available at $outDir/$logfile"