.run(function($ionicPlatform) {
    $ionicPlatform.ready(function($rootScope, $ionicPopup, $timeout) {

    // Code here
    ....

    $rootScope.showAlert = function() {
       var alertPopup = $ionicPopup.alert({
         title: 'Don't eat that!',
         template: 'It might taste good'
       });

       alertPopup.then(function(res) {
         console.log('Thank you for not eating my delicious ice cream cone');
       });
    };

    // Code here
    ....
});

<button ng-click="$root.showAlert()">