I noticed your e-mail and as Katherine is away today, I thought I could
respond to the following bit.
You wrote:

> setting JAVA_HOME*: I tried several paths (/usr/bin; /usr/lib....)
that I found using *find* command:
> /usr/bin/java
> /usr/lib/java
> /usr/java
> /usr/java/bin/java
> /usr/java/jre/bin/java

> changing *gli.sh* and *gems.sh* to set *"javapath*=" to the right
path, but I couldn't find the exact line to do that;

Perhaps, as per your own idea, we can work backwards to find out what
javapath needs to be set to.

Ultimately, the launch command comes at the very end of the gli.sh file.
Look for a (comment) line like the following in gli.sh
# -Xloggc:<file> Write garbage collection log

After this, there will be line setting the exit_status to 0 and then
come the commands to launch GLI,
which use $javapath to run GLI with.

So, if after the "#-Xloggc" comment you could add a line like this:
export javapath=
Or just:
javapath=

And then after the "=" sign, insert one of the .../bin/java paths you've
listed above,
for instance /usr/java/bin/java (or /usr/bin/java or even
/usr/java/jre/bin/java).
You can try them all out in turn to see if any gives a working result:
save the file and run ./gli.sh
from the "gli" folder to see whether it stops complaining about Java
using on any of the bin/java paths

If you've found a bin/java path that works for you, try it also with gems.sh
For this, find the line that starts with:
basic_command="$javapath -classpath classes/:GLI.jar:lib/apache.jar
org.greenstone.gatherer.gems.GEMS"

Then, just before that line, set javapath:
javapath=<here, insert your ...../bin/java>
Save the file and try run ./gems.sh from the "gli" folder.

If the above worked, then we would still need to figure out why
"findjava.sh" in both your Greenstone and
its "gli" folders didn't pick up on this.

One more thing that may be important to mention is that the version of
Java that Greenstone wants is a Sun
Java. Therefore, is the Java installed on your machine a Sun
(Microsystems) Java?

Regards,
Anupama of the Greenstone Team