It is straightforward to set up Modeller to work with the module command, for example as provided by Environment modules or Lmod. Here is an example modulefile:
#%Module 1.0
module-whatis "Description: MODELLER comparative modeling"
module-whatis "URL: https://salilab.org/modeller/"
set topdir <MODELLER INSTALL DIR>
prepend-path PATH ${topdir}/bin
prepend-path LD_LIBRARY_PATH ${topdir}/lib/x86_64-intel8
prepend-path PYTHONPATH ${topdir}/lib/x86_64-intel8
prepend-path PYTHONPATH ${topdir}/modlib
prepend-path PKG_CONFIG_PATH ${topdir}/lib/x86_64-intel8/pkgconfig
Replace <MODELLER INSTALL DIR> with the directory where you installed Modeller, and put the resulting file somewhere in your system's MODULEPATH.