installation of Jemboss from EMBOSS-2.6.0 package questions

[Jerry Mullersman]

I have been trying to install Jemboss in standalone mode from the EMBOSS-2.6.0
package on a Mandrake 9.0 i586 system.  First, let me say that I can complile
and install EMBOSS with no problems on this system.  However, repeated attempts
to install Jemboss have failed. One thing that is not very clear to me in the
Jemboss intallation is the exact meaning of some of the setup prompts; I'm
concerned that I may not be answering these prompts correctly and, cosequently,
be causing the installation to fail.  For instance, what is the meaning of
"Enter java (1.3 or above) location [/usr]"?  There is a "java" directory in
/usr and it contains links to a jre-1.3.1_04 directory in /usr/lib.  So, is it
correct for me to accept the default answer /usr?  Likewise, what is the
meanining of "Enter EMBOSS download directory"?  Does this refer to the
EMBOSS-2.6.0 directory that is created by extracting the EMBOSS-2.6.0.tar file
or to the directory above it?  Finally, what is the best answer to "Enter where
EMBOSS should be installed [/usr/local/emboss]"?  In my case, the
EMBOSS-2.6.0.tar file was extracted in /usr/local/emboss.  My recollection is
that the straight EMBOSS installation puts EMBOSS in /usr/local and its
subdirectories.  Wouldn't that be best for the Jemboss/EMBOSS installation,
also?

I haven't been able to find an explanation of these points in the available
documentation, and it doesn't appear that these questions have been raised on
the list during the last year (which makes me suspect that these are
silly/stupid/dumb/nitwit questions).  Thanks for your help.

Jerry Mullersman


=====
Jerald E. Mullersman, MD, PhD
Associate Professor
Department of Pathology
East Tennessee State University
PO Box 70568
Johnson City, TN 37614
phone: (423) 439-6210   fax:  (423) 439-8060