install modules with custom module
If you define the modules in the subdirectory as dependencies of your main module, then they'll be enabled once your "controller" module is.

i.e.

name = Really Neat Widget
description = Provides a really neat widget for your site's sidebar.
core = 7.x
package = Views
dependencies[] = MODULE_ONE
dependencies[] = MODULE_TWO


Source

Alternatively, you could take a look at the Master module.