If you are asking for some way to password-protect a shell script when it runs, then it requires a little more coding in....
You didn't specify which language you're using...but if this is a BASH script, here's a link that provides a method to do this at runtime, checking the password against a second file:
Prompting users for passwords in a shell script? :: Free Tech Support :: Ask Dave Taylor!
Of course you can modify the arguments to fit whatever language you are running it under....
This would of course only work if you disable most access to the password file you make. I wouldn't suggest putting the password explicitly in the file since you've given read access to it...
For the sake of thoroughness, if you do decide to block read access to the file, here's an example using md5sum to check the password. Please note I'm half awake at the moment, so there's more than likely some way to make this look a little more elegant, but this runs when I test it on my machine
Once again using bash:
#!/bin/bash
echo -n "Enter password: "
read -e VALUE
TEST=`echo -n $VALUE|md5sum`
pwdchk="5f4dcc3b5aa765d61d8327deb882cf99 -"
if [ "$TEST" = "$pwdchk" ]; then
echo "the program will run"
else
echo "The program will not run"
fi