Comment 4 for bug 1547519

A workaround is to create a symlink (named etc) to /etc/circos in the directory that contains the configuration files for a given circos plot. This makes the suggested patch unnecessary. It additionally preserves the ability to use relative includes for other circos configuration files.

In my opinion, the best solution would be to add /etc/circos to circos' search path, though.
See also: http://circos.ca/tutorials/lessons/configuration/configuration_files/