[EMBOSS] EMBOSS and Jemboss installation problems

[Pierre Scotney]

Hello,

I am having problems installing EMBOSS and Jemboss.  I have read all the 
INSTALL and README docs in the EMBOSS-2.8.0 directory and the web docs for 
Jemboss standalone installation, so please no RTFM responses :)

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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