pass parameters drush_make or drush_make_process
The most stable way to call Drush from a php script is to use drush_invoke_process.

For example:

$values = drush_invoke_process('@none', 'make', array('someFile.make'), array('no-core' =&gt; TRUE, 'contrib-destination' =&gt; 'sites/all', 'yes' =&gt; TRUE));