Hello,
I am part of a small group of people engaged in packaging mathematical software for the Fedora Linux distribution. I've been looking at polymake recently. The first challenge is that the nauty license does not permit redistribution by Fedora. I have attempted to port polymake to bliss instead. I'll attach a patch against polymake 2.11. This is not well tested yet, so further changes may prove necessary, but I'll provide it for anybody else facing the same problem.
Another challenge with the nauty license is that it doesn't even permit distribution of the source code by Fedora. So if I succeed in making a package, I will have to download your tarball, remove the nauty sources, re-tar, and use that as input to the Fedora build process. Since Fedora doesn't permit bundled libraries in any case, from my viewpoint, it would be great if you could provide a tarball (aimed at distributions) that does not contain the "external" directory, since the first thing I'll do is remove it anyway.
Some of the bundled libraries are at http://jjames.fedorapeople.org/ while they go through the Fedora review process.
Regards,
--
Jerry James