[kepler-users] wrapping command-line tools

[Luciana Gomes]

Hello Matt,

Thanks a lot for your answer.

So, I was already executing BLAST using External Execution actor. But I'd
like to have a 'blast' actor that receives through ports the blast inputs
(database and input sequences). I've tried to customize the External
Execution actor adding a 'inputsequences' port, but I think this should be
a PortParameter type, so I can read it inside a parameter and put it in
the command line, so I'd have:

- a PortParameter called 'inputsequences'
- a Parameter called 'inputsequences'
- and the command would be: blastall -i $inputsequences

Would this work? I don't figure out how to add a PortParameter using
'configure ports' option.

Just some other doubts if you can help:

1- If I customize External Exec actor this way, how could I transform it
into another independent actor, with a new lsid?

2- I've made some changes in the actor and I've exported it as .kar. How
do I use this 'new' actor in other workflows?

3- Does this 'new' actor created in item 2 continue using the external
exec class, or is it loaded and called only using the moml exported?

4- How do I 'edit' an actor changing directly its code (java or moml?) ??

Thanks a lot,
Luciana


> Hi Luciana,
>
> On Thu, Feb 24, 2011 at 10:47 AM, Luciana Gomes
> <lgomes at inf.puc-rio.br>wrote:
>
>> Hello,
>>
>> do you have some example of an actor that encapsulates a command-line
>> tool, like BLAST tool?
>>
> There are two examples of using the External Execution actor to execute an
> external program and return the results.  See the Getting Started Guide
> examples.  Example 07 shows how to run a java HelloWorld program, and
> example 08 shows how to run the R system.  Either demo could be easily
> adapted to run the Blast tool.  You can find the demos in your KeplerData
> folder in your home directory:
>   KeplerData/workflows/module/outreach-2.1.0/demos/getting-started/07-CommandLine_1.xml
>   KeplerData/workflows/module/outreach-2.1.0/demos/getting-started/08-CommandLine_2.xml
>
>
>> Is it possible to make this kind of actor outputs a file, which is for
>> example the alignment file generated by BLAST, considering this can be a
>> big file?
>>
> The external execution actor will pass along anything that comes out of
> STDOUT to the output port of the actor.  If you are concerned about file
> size, the easiest thing to do would be to arrange for your commandline
> tool
> to output a filename that is processed downstream by other actors as
> needed.
>
>
>> Would this file be stored in DATA table of provenance database?
>>
> The provenance DB captures port outputs, so as far as I know it would be
> stored if provenance is on.
>
> Matt
>
>>
>> Thanks a lot,
>> --
>> Luciana
>>
>>
>>
>>
>>
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>>
>


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