biopython and jython

$ jython setup.py build
$ jar cvf BioPython.jar -C build/lib ./

Include the produced jar file in your CLASSPATH or server build.

Have you run "jython setup.py install" yet? That will compile the *.py
files into Java class files, and should put them where jython looks.

See also:
http://www.jython.org/docs/using/cmdline.html#environment-variables

... from the biopython-dev mailist