Request to add make flags to the make install command

Occasionally, the "make install" command requires custom flags, just like the "make" command.  The specific use case for this request is for building programs like ATLAS which require being built inside a separate build directory.  Make's "-C" flag makes this incredibly easy by changing to the specified directory prior to executing the make command.  

As an example, say qiime-deploy is sitting inside the ~/ATLAS/ directory but needs to execute the make command from within ~/ATLAS/build_dir/.  Running the follow commands from the ~/ATLAS/ directory accomplishes this task: 

     make -C build_dir ; make install -C build_dir.  

The required code change is simply to add the customMake flags to the "make install" command.