Kris Wallsmith (maker of assetic) helped me out doing this, and helped me in the right direction.
$asset = new FileAsset(__DIR__ . '/../Resources/assets/script.js');
$closureFilter = new CompilerJarFilter(
$this->getContainer()->get('kernel')->getRootDir() . '/Resources/java/compiler.jar'
);
$closureFilter->setCompilationLevel(CompilerJarFilter::COMPILE_ADVANCED_OPTIMIZATIONS);
$asset->ensureFilter($closureFilter);
$script = $asset->dump();