On 29/07/10 16:51, Stuart Owen wrote:
> Hi Mark,
>
> try : dot -Tdia test.dot
>
Sorry, dia was a bad one to use as its a binary output. Instead, try :
dot -Tmif 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
>>>
>>>
>>>
>>>
>>>
>>
>>
>
> ------------------------------------------------------------------------------
> 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/
>
------------------------------------------------------------------------------
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/
