UNIX for Dummies Questions & Answers

#include <iostream>
#include <fstream>
#include <string>
using namespace std;

int main(int argc, char* argv[]) {

string file_name;
string run_num;
string config_file;
int opt = 0;

for (int i = 1; i < argc; i++) {
           if (i + 1 != argc)
               if (argv[i] == "-dir") {
                   file_name = argv[i + 1];
               } else if (argv[i] == "-run") {
                   run_num = argv[i + 1];
               } else if (argv[i] == "-mask") {
                   opt = 1;
               } else if (argv[i] == "-cfg") {
                   config file = argv[i+1];
               }
           std::cout << argv[i] << " ";
       }

if (opt == 0){
// Unix commands for unmasked
}

if (opt == 1){
// Unix commands for unmasked
}

return 0;
}

#!/bin/sh

OPT=0

while [ "$#" -gt 0 ]
do
        case "$1" in
        -cfg) cfg_file=$2; shift ;;
        -dir)  file_name=$2; shift ;;
        -run) run_num=$2; shift ;;
        -mask) OPT=1 ;;
        *)     break ;;
        esac

        shift
done

if [ -z "$cfg_file" ]
then
        echo "No config file given" >&2
        exit 1
fi

if [ -z "$file_name" ]
then
        echo "No file name given" >&2
        exit 1
fi

if [ -z "$run_num" ]
then
        echo "No run number given" >&2
        exit 1
fi

if [ "$OPT" -eq 1 ]
then
        ../../bin/takeData -l -dir $file_name -trimVcal 60
        ...
else
        ../../bin/takeData -l -dir $file_name -trimVcal 60
        ...
fi

OPT=0
OP=0

while [ "$#" -gt 0 ]
do
        case "$1" in
        -cfg) cfg_file=$2; shift ;;
        -dir)  file_name=$2; shift ;;
        -run) run_num=$2; shift ;;
        -mask) OPT=1 ;;
        -root) OP=1 ;;
        *)     break ;;
        esac

        shift
done

if [ -z "$cfg_file" ]
then
        echo "No config file given" >&2
        exit 1
fi

if [ -z "$file_name" ]
then
        echo "No file name given" >&2
        exit 1
fi

if [ -z "$run_num" ]
then
        echo "No run number given" >&2
        exit 1
fi

if [ "$OPT" -eq 1 ]
then
        ../bin/takeData -l -dir $file_name -trimVcal 60 -mask
        cd ../convert_to_tree/
        cp $file_name/phCalibrationFitTan_C0.dat $file_name/phCalibrationFit60_C0.dat
        cp $file_name/phCalibrationFit60_C0.dat ~/log/bt0500$run_num
        cp ../convert_to_tree/config.dat_original ~/log/bt0500$run_num
        ./convert_to_tree -l -r $run_num
        ./pulseHeightMain $run_num

if [ "$OP" -eq 1 ] 
        then 
                cd ~/log/bt05r00$run_num 
                root -l 
else 
        ../bin/takeData -l -dir $file_name -trimVcal 60 
        cd ../convert_to_tree/ 
        ./Analyze.py --dir $file_name --cfg $cfg_file $run_num 
         
        if [ "$OP" -eq 1 ] 
        then 
                cd ~/log/bt0500$run_num 
                root -l 
fi

# This only needs to be done once, ever.  It sets the file executable, so it can be run.
chmod +x ./myscript.sh

# The arguments don't need to be in any order, except that cfgname must be straight after -cfg, etc.
./myscript.sh -cfg cfgname -dir dir -run 3 -mask -root

command1
command2
command3

case "$something" in
-h)
        something
        something else
        yet more commands
        exit # to quit immediately, so it doesn't try to run commands below
        ;;
esac