[EMBOSS] EMBOSS and Jemboss installation problems

[Dr T. Carver]

Hi Pierre

The problem is likely to be that you precompiled emboss before running
the install script. There is no need, the install script does this for
you with the correct java flags. Try a 'make clean' and then run the
install script.

Hope this helps.
Regards
Tim Carver

RFCGR

>
> I am building EMBOSS-2.8.0 on a GNU/Linux system (Mandrake 9.1) with
> Blackdown Java j2sdk-1.3.1-02b-FCS-linux-i386 installed and running ok.  I
> have installed zlib-1.2.1 libpng-1.2.5 and gd-2.0.22 so all the libraries
> and includes are present.
>
> I build as root with the following commands:
>
> cd EMBOSS-2.8.0
> ./configure --prefix=/usr/local/emboss
> make
> make install
> cd jemboss/utils
> ./install-jemboss-server.sh
>
> selecting the option (2) STANDALONE and the rest of the prompts.  The
> generated /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh and
> /usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties files
> all look ok with the correct paths.
>
> I have added /usr/local/emboss/{bin,lib} to the PATH and ld.so.conf
> respectively and wosname -auto is working:
>
> ALIGNMENT CONSENSUS
> cons             Creates a consensus from multiple alignments
> megamerger       Merge two large overlapping nucleic acid sequences
> merger           Merge two overlapping nucleic acid sequences
> etc.....
>
> but when I
>
> cd /usr/local/emboss/share/EMBOSS/jemboss
> ./runJemboss.sh
>
> all I ever get is the following error:
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/emboss/jemboss/Jemboss
>
> What have I done wrong?  Please help!
>
> Regards
>
> Pierre
>
>
> --
> Dr Pierre Scotney
> Melbourne
> Australia
>
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