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Yes, you can specify dependencies in your migration code. For example

class MySiteProgramNodeMigration extends MySiteMigration {
public function __construct() {
parent::__construct();

$this->description = t('Migration for Program nodes');
// Define source fields for the migration
$source_fields = array('nid' => t('The node ID of the Program node.'));
// The user migration should run first, so that we can associate nodes
// with Drupal users
$this->dependencies = array('MySiteUser');

The Migrate Examples module has some more examples of this. We were running into issues with this though, and since we had a script in place for rebuilding the site, it was much more time efficient to call the migrations individually than to spend the time to debug our problems with Migrate module.

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