Hi Mark,
try : dot -Tdia test.dot
then try: dot -Tsvg test.dot
I have a suspicion your dot doesn't output svg, as when i miss the
output option I get:
Format: "marks.dot" not recognized. Use one of: canon cmap cmapx
cmapx_np dia dot eps fig gd gd2 gif hpgl imap imap_np ismap jpe jpeg jpg
mif mp pcl pdf pic plain plain-ext png ps ps2 svg svgz tk vml vmlz vrml
vtx wbmp xdot xlib
Stuart.
On 29/07/10 16:48, Mark Wilkinson wrote:
> 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
>>
>>
>>
>>
>
>
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