[Bio-Linux] Re: [Taverna-users] taverna on Bio-Linux

[Tom Oinn]

Bela Tiwari wrote:
> Hello Tony,
> 
> I've posted this response to the taverna-users mailing list also in
> case anyone has any comments about the issue you saw.
> 
>> I've installed it from the *.deb repository on
>> wildcat.rri.sari.ac.uk under Debian 'stable' (i.e not under
>> Bio-Linux) but it crashed and burned: can't find the plugins
>> folder. Anyone else had this problem?

That's nothing to worry about - Taverna 1.3 has a partially working
alternate classloader, what you're seeing is the debug output. The
'can't find the plugins folder' message is present on all platforms, it
shouldn't have any impact on functionality of the code though.

> The bio-linux-taverna package includes a runme_biolinux.sh file which
> is what is being called when you run taverna after installing the
> package. That file is very similar to the standard runme.sh file that
> comes with taverna - it was just hacked a bit (by me...so you know
> who to blame) to make Taverna run sensibly on a multi-user system
> like Bio-Linux.
> 
> Another person here, Chimdi Ekeke, tried to run Taverna (installed
> from the Bio-Linux package) on a non-Bio-Linux version of Debian
> (stable) and saw the same issue as you. He then tried running it
> using the standard runme.sh script (from an appropriate location) and
> this caused the same problems, which suggests this might be a problem
> with Taverna 1.3 on standard Debian Sarge installations.
> 
> If you alter the java command at the very end of the
> runme_biolinux.sh to rearrange the order of the -D flags such that it
> looks like:
> 
> -Dtaverna.home=$TAVERNA_HOME -ea
> org.embl.ebi.escience.scuflui.workbench.Workbench
> 
> taverna will work, but according to Chimdi, it then takes on a
> similar appearance to Taverna version 1.2 rather than what is it,
> version 1.3.

That would be rather strange, the only way the code could be picking up 
1.2 behaviours would be to have the 1.2 code present somewhere - they 
just don't exist in 1.3. You might get a different look and feel if 
you're running different versions of Java but that's the only thing I 
could think of that would account for it. You might have to be more 
specific on 'takes on a similar...' etc though, it's rather hard to tell 
what the problem is.

On Java 5 and linux you need to remove the -Dtaverna.scrolldesktop (or 
similar) from the command line, this disables a feature that has issues 
with some look and feel classes on JDK5.

Tom