[Biopython] biopython and jython

[Peter]

On Thu, May 20, 2010 at 4:18 PM, Silvio Tschapke wrote:
> Thanks for your fast reply...
>
>> > I am using Java Servlets in tomcat and Jython and thought there won't be
>> > problem to call Biopython modules from Jython. But Biopython is not
>> > included
>> > in jython.jar.
>>
>> I think there is a Jython path environment variable you can set...
>
> You mean I have to set Jython class or system path? And point it to:
> python26/libs/site-packages/Bio ?
>
> Because I am running my project on tomcat (I have copied jython.jar into
> tomcat/libs) I have to tell Tomcat where it can find the Bio package. Don't
> I ? Biopython installs itself under python26/lib/site-packages, so there is
> no .jar which I could copy into tomcat/libs).

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

Peter