Here's the result:
{feynman}/usr/bin/dot -T test.dot
Format: "test.dot" not recognized. Use one of: dia hpgl mif mp pcl pic vtx
{feynman}cat test.dot
digraph "Workflow1" {
graph [
bgcolor="#ffffff"
color="black"
fontsize="10"
labeljust="left"
clusterrank="local"
ranksep="0.22"
nodesep="0.05"
]
node [
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"
];
"Workflow1runEmbossConsFromAlignment" [
fillcolor="#ffb90f"
style="filled,solid"
shape="box"
width="0.0"
height="0.0"
label="runEmbossConsFromAlignment"
];
}
So apparently dot doesn't recognize the text that Taverna is exporting...
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
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