[Bio-Linux] taverna on Bio-Linux

[Bela Tiwari]

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?

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.



cheers

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


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