[Bioperl-l] Bioperl Vista module and CGI

[Jonathan Manning]

Sorry, sent that ages ago, seems to have rematerialised from somewhere!
I solved it by giving java a CLASSPATH argument via the Vista wrapper.

Jon

On Thu, 2004-07-29 at 05:59, Joel Martin wrote:
> Hello,
> 	This is just a stab in the murk but usually if you want
> to set an environmental variable in perl you set it in the %ENV 
> hash, what you're doing looks like it would only apply to that
> system call (disappearing as it returns).
> $ENV{CLASSPATH} = "$ENV{CLASSPATH}:/usr/java/j2sdk1.4.2_04/lib/Vista.jar";
> and I'm sometimes confused about whether or not to wrap that in 
> a BEGIN statement (don't think it would hurt) like before you "use"
> anything:
> BEGIN{$ENV{CLASSPATH} =
> "$ENV{CLASSPATH}:/usr/java/j2sdk1.4.2_04/lib/Vista.jar";}
> 
> Joel
> On Tue, Jul 06, 2004 at 04:20:15PM +0100, Jonathan Manning wrote:
> > Hi to all,
> > 
> > Sorry if the Bioperl relevance of this is fairly limited, but I thought
> > someone here might have come across the same problem.
> > 
> > I'm using the bioperl module wrapper for Vista, and was trying to plug
> > it into a CGI script. The trouble is my Apache server can't 'see' the
> > java class library of Vista- presumably because it doesn't have access
> > to the user CLASSPATH, and I get an error like: 
> > java.lang.NoClassDefFoundError: Vista.  
> > 
> > I've tried:
> > 
> > system("export
> > CLASSPATH=$CLASSPATH:/usr/java/j2sdk1.4.2_04/lib/Vista.jar"); 
> > 
> > from within the script without success. The script works fine when run
> > from the command line.
> > 
> > Thanks- appreciate any pointers,
> > 
> > Jon
> > 
> >  
> > 
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>