running Jemboss after EMBOSS installation

[Dr T. Carver]

Hi Fernan

There is an install script provided in EMBOSS-2.6.0/jemboss/utils, that
installs EMBOSS and Jemboss (along with Tomcat and Axis if you are doing
a server installation). It compiles EMBOSS with the --with-java and
--with-javaos flags and --with-thread=$PLATFORM. The script compiles
Jemboss and adds the Axis library to Tomcat. It will also deploy the Axis
(SOAP) methods that Jemboss can access.

The script is described further at:

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/setup.html

If you do a plain EMBOSS installation Jemboss is not installed at all.

Hope this helps.
Best regards
Tim Carver


> 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
>