in config.php , its possible to make another variable and call it in view
$root="http://".$_SERVER['HTTP_HOST'];
$root.=str_replace(basename($_SERVER['SCRIPT_NAME']),"",$_SERVER['SCRIPT_NAME']);
$config['base_url'] = $root;
$config['img_url']=$root.'assets/img/';
$config['jsctrl_url']=$root.'application/JsController/';
and call it like
<script type="text/javascript" src="<?php echo jsctrl_url();?>Account/register.js"></script>
What you need is a constant and not a function like base_url.
Head on to your config/constants.php and create a new one like:
$root ="http://".$_SERVER['HTTP_HOST'];
$root .= str_replace(basename($_SERVER['SCRIPT_NAME']),"",$_SERVER['SCRIPT_NAME']);
$config['base_url'] = $root;
define('IMG_URL', $root . 'assets/img/');
define('JS_URL', $root . 'application/JsController/');
Then in your views you would use it as a normal constant.
<script type="text/javascript" src="<?php echo JS_URL ?>Account/register.js"></script>
