Each submodule gets its own portfile.

scripts/Portfile

-# $Id$
-
-PortSystem              1.0
-
-name                    moose
-version                 3.0.2
-categories              science
-platforms               darwin
-maintainers             dilawars \
-                        ncbs.res.in:dilawars
-description             MOOSE is the Multiscale Object-Oriented Simulation \
-                        Environment.
-long_description        MOOSE is the Multiscale Object-Oriented Simulation \
-                        Environment.
-
-homepage                http://moose.ncbs.res.in
-fetch.type              git
-fetch.ignore_sslcert    yes
-git.url                 https://github.com/BhallaLab/moose-core
-git.branch              master
-license                 GPL-3
-
-
-depends_build           port:cmake \
-                        port:python27 \
-                        port:gsl  \
-                        port:hdf5 \
-
-depends_lib             port:gsl \
-                        port:hdf5 \
-                        port:py27-matplotlib \
-                        port:py27-numpy \
-                        port:python27 \
-
-set python_branch       2.7
-
-configure.cmd {
-    mkdir -p _build
-    cd _build 
-    cmake -DCMAKE_INSTALL_PREFIX=${prefix} ..
-}
-configure.args          VERBOSE=1 
-configure.pre_args      ""
-configure.post_args     ""
-
-build.cmd               cd _build && make 
-build.pre_args          ""
-build.post_args         ""
-
-test.cmd                cd _build && ctest --output-on-failure