One of the way you can run script tags in php would be
<?php
....Here is php code
?>
... add the script here(<script>....</script>
<?php
?>
Another probable way is :
Using php inside the script tags for example:
<script type="text/javascript">
var alertMsg = '<?php echo $custom_message; ?>';
alert(alertMsg);
</script>
If you are using buttons
echo('<button type="button" onclick="customfunction();">My Button</button>');
<script>
//call your customfunction here
</script>
AN UPDATE TO SOLVE LOADING SCRIPT CONTENTS TWICE
I would suggest use of javascript function which are called to the specific page as they are needed an example would be
Create a file with a .js eg
example.js
here declare your functions you would put in the script tags of a html page
In the page you want to use the <script>
Include the example.js file and you can call the custom functions from there use the obect orientend approach
Check This resource for more info about obect orientend javascrip