Bioinformatic app can't find JVM

[Tommy Pham]

--- KAYVEN  RIESE <kayve at sfsu.edu> wrote:

> 
> This website:
> 
> http://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 $PATH
>
/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/root/bin
> kv_bsd#cp apolloinst.bin /usr/home/kayve
> kv_bsd#
> kv_bsd#uname -a
> FreeBSD kv_bsd 6.2-RELEASE FreeBSD 6.2-RELEASE #0: Fri Jan 12
> 10:40:27 UTC 
> 2007     root at dessler.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC 
> i386
> kv_bsd#
> [kayve at kv_bsd ~]$ java sdf
> Exception in thread "main" java.lang.NoClassDefFoundError: sdf
> [kayve at kv_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