Sorry - reading my messages in reverse order :-) I'll try this.
M On Thu, 29 Jul 2010 00:14:34 -0700, Stian Soiland-Reyes <[email protected]> wrote: > On Wed, Jul 28, 2010 at 17:50, Mark Wilkinson <[email protected]> > wrote: > >> Scientific Linux 5.2 an x86_64 server with 8 CPUs and 48 Gb RAM > > Now we're talking.. putting the 'heater' MacPro under my desk to > shame, it has only 16 GB and runs 5-6 virtual machines! > > However, as the Scientific Linux 5.2 ISO is 4.4 GB I won't easily be > able to test this distro in a VM while working from home today.. > > >> WARN 2010-07-28 12:35:57,273 >> (net.sf.taverna.t2.workbench.models.graph.svg.SVGGraphController:182) - >> Invalid dot returned > > String layout = SVGUtil.getDot(stringWriter.toString()); > if (layout.equals("")) { > logger.warn("Invalid dot returned"); > > So it means an empty string was returned, very mysterious. > > Could you try View -> Save diagram -> Save as dot text - and then on > the command line try to run 'dot' on the saved DOT file: > > : st...@ralph ~/Desktop; dot -Tdot diagram.dot > > digraph Workflow1 { > graph [bgcolor="#ffffff", color=black, fontsize=10, labeljust=left, > clusterrank=local, ranksep="0.22", nodesep="0.05"]; > node [label="\N", fontname=Helvetica, fontsize=10, fontcolor=black, > shape=record, height=0, width=0, color=black, > fillcolor=lightgoldenrodyellow, style=filled]; > edge [fontname=Helvetica, fontsize=8, fontcolor=black, color=black]; > graph [bb="0,0,58,20"]; > Workflow1Beanshell [label=Beanshell, shape=box, height="0.28", > width="0.81", fillcolor="#deb887", style="filled,solid", pos="29,10"]; > } > > (Here we can see Graphviz as determined the positions of the boxes in > a very simple workflow with a single Beanshell script) > > >> Which config file should I be looking at for rogue spaces? > > See > ~/.taverna-2.2.0/conf/Workbench-c14856f0-5967-11dd-ae16-0800200c9a66.config > > For example: > > #Wed Jul 28 17:24:49 BST 2010 > taverna.dotlocation=/usr/bin/dot > > > -- -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, BC, Canada ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ Developers Guide: http://www.taverna.org.uk/developers/
