Bioinformatic app can't find JVM

This website:

htt
p://www.fruitfly.org/annot/apollo/install.html

has an installation script called apolloinst.bin
with instructions to install as seen in command
line clip that includes BSD info and my personal
"error" diagnostic showing java is there:

[::clip::]

kv_bsd#sh ./apolloinst.bin
Preparing to install...
Extracting the installation resources from the installer
archive...
Configuring the installer for this system's environment...
No Java virtual machine could be found from your PATH
environment variable.  You must install a VM prior to
running this program.
kv_bsd#echo $PATH
/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/us
r/local/bin:/usr/X11R6/bin:/root/bin
kv_bsd#cp apolloinst.bin /usr/home/kayve
kv_bsd#
kv_bsd#uname -a
FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri Jan
12 10:40:27 UTC 
2007     rootdessler.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC 
i386
kv_bsd#
[kayvekv_bsd ~]$ java sdf
Exception in thread "main"
java.lang.NoClassDefFoundError: sdf
[kayvekv_bsd ~]$

[::end clip::]

I have already tried adding


JAVA_HOME="/usr/local/bin/java"

to the apolloinst.bin file with no results.

Thank you for your help.

*----------------------------------------------------------*

   Kayven Riese, BSCS, MS (Physiology and Biophysics)
   (415) 902 5513 cellular
   http://kayve.net
   Webmaster http://ChessYoga.org
*----------------------------------------------------------*

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--- KAYVEN  RIESE <kayvesfsu.edu> wrote:

> 
> This website:
> 
> htt
p://www.fruitfly.org/annot/apollo/install.html
> 
> has an installation script called apolloinst.bin
> with instructions to install as seen in command
> line clip that includes BSD info and my personal
> "error" diagnostic showing java is there:
> 
> [::clip::]
> 
> kv_bsd#sh ./apolloinst.bin
> Preparing to install...
> Extracting the installation resources from the
installer archive...
> Configuring the installer for this system's
environment...
> No Java virtual machine could be found from your PATH
> environment variable.  You must install a VM prior to
> running this program.
> kv_bsd#echo $PATH
>
/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/us
r/local/bin:/usr/X11R6/bin:/root/bin
> kv_bsd#cp apolloinst.bin /usr/home/kayve
> kv_bsd#
> kv_bsd#uname -a
> FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri
Jan 12
> 10:40:27 UTC 
> 2007     rootdessler.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC

> i386
> kv_bsd#
> [kayvekv_bsd ~]$ java sdf
> Exception in thread "main"
java.lang.NoClassDefFoundError: sdf
> [kayvekv_bsd ~]$
> 
> [::end clip::]
> 
> I have already tried adding
> 
> 
> JAVA_HOME="/usr/local/bin/java"
> 
> to the apolloinst.bin file with no results.
> 
> Thank you for your help.
> 
>
*----------------------------------------------------------*

>    Kayven Riese, BSCS, MS (Physiology and Biophysics)
>    (415) 902 5513 cellular
>    http://kayve.net
>    Webmaster http://ChessYoga.org
>
*----------------------------------------------------------*


Hi Kayven,

I think you didn't set the environment correctly.  Depending
on which
JVM you've installed, the JDK should be in at the default
location on
FreeBSD:

/usr/local/diablo-jdk1.5.0
/usr/local/jdk1.5.0
/usr/local/jdk1.6.0

To set your environment, if you use the default csh shell:
  setenv JAVA_HOME /usr/local/diablo-jdk1.5.0
or
  setenv JAVA_HOME /usr/local/jdk1.5.0
or
  setenv JAVA_HOME /usr/local/jdk1.6.0

If you're using bash shell:
  JAVA_HOME=/usr/local/diablo-jdk1.5.0
or
  JAVA_HOME=/usr/local/jdk1.5.0
or
  JAVA_HOME=/usr/local/jdk1.6.0
then
  export $JAVA_HOME

I hope this help.

Regards,
Tommy
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