Trying to create a cron job to run if a condition is true

I'm not sure what to use for my path to codeigniter in the cron job.
In my index.php I have my $application_folder = '../../codeI/application'; Is this what I should set as my path to codeigniter in the cron job also?

No, for the cronjob you'd need the full filepath up to and including "index.php". Cron doesn't know anything about your relative application path, and actually you don't want to use the application dir anyway...just the path TO index.php.

If you don't know the full path, you can open up index.php and scroll down towards the bottom, you will see a define('FCPATH', str_replace(SELF, '', __FILE__)); or something similar.
just under that line put die(FCPATH) and visit your site. It will give you the full path to your CI dir. Be sure to remove that line after you do this.

Something like /home/some_user/public_html/

Then just add an index.php to the end of that and that's what you'd want to use for your cronjob.
/home/some_user/public_html/index.php.