running Jemboss after EMBOSS installation

[Fernan Aguero]

Hi!

I finally got EMBOSS-2.6.0 and all the EMBASSY packages
ported to FreeBSD. I am about to submit the port to the
FreeBSD ports system. However, I have some issues with
Jemboss:

Apparently all of the jemboss stuff gets installed in
appropriate places. I see an ELF binary (jembossctl) and a
shell script (runJemboss.csh) in PREFIX/bin; and a whole
tree of various things at PREFIX/share/EMBOSS/jemboss

i) is it everything ready to run Jemboss? I have both a
native jdk (v1.3.1) and a linux-jdk (v.1.3.1) and with
either of these I get the same error:
[fernan at pi] /var/tmp/port_test/bin/runJemboss.csh
[fernan at pi] Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss
Or perhaps I should tweak some files manually?
The runJemboss.csh file has all instances of PREFIX
correctly replaced by /var/tmp/port_test (the PREFIX I used
to test everything).

ii) I noticed that the runJemboss.csh script that gets
installed into PREFIX/bin differs from the one in
PREFIX/share/EMBOSS/jemboss, and I also saw some
instructions at the web site, regarding both standalone and
client-server modes ... it is not clear to me which one I'm
going to get with a plain EMBOSS installation.

Thanks in advance for any tip or suggestion,

Fernan

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan