How might I run make_fragments.pl without first installing sparks?
I am working with the rosetta_2014.16.56682 weekly release.
I have not tried this myself, but you may be able to provide an empty string for the SPARKS variable at line 43 in the make_fragments.pl script. You'll also probably have to comment out the SPARKS lines at line 97 and the SPARKS block at 126-128.
You'll also want to make sure you have all the other dependencies installed, otherwise the (automatically invoked) Rosetta/tools/fragment_tools/install_dependencies.pl script will attempt to install it. (You could also comment out the SPARKS lines there, too: lines 117-171, which would prevent the automatic installation.)