[kepler-users] wrapping command-line tools

[Matt Jones]

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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