Re: [Opaltoolkit-users] Sequential Execution

[Luca C. <luc...@gm...>]

Dear Jeffry,
please see below...

On Mon, Apr 9, 2012 at 10:29 AM, Jeffrey Allen
<Jef...@ut...> wrote:
> Hello,
>
>
>
> My group has been working on developing an execution pipeline for
> Bioinformatics programs. We’ve been considering using SOAP to handle the
> input parameters for the individual programs; it seems that Opal could be a
> good foundation for us to use if we go this direction.
>
>
>
> My question, however, is whether or not there are any built-in or external
> projects that offer some control of the “flow” of execution of submitted
> commands. For instance, a user may submit requests A, B, and C, but would
> like to specify that B and C depend on the output of A. Thus, the proper
> execution would be to begin A immediately, then begin B and C once A has
> completed.
>
>
>
> I’d be interested to hear any advice this group has on how to proceed with a
> project like this. Is this something which could be built on top of Opal,
> should I consider trying to incorporate this directly into Opal, or is there
> another platform which I should consider using?

It really depends what do you have to do...

If you workflow is as simple as you said above and you need to
integrate this calls into your "client" (some customized GUI) I would
use one of the Opal client side library and simply invoke A, B, C
sequentially in the code.
We have Opal client side libraries for perl java and python (Im
currently writing a higher level python API for Opal).

You can chain A B C in the script that gets invoked by Opal service D
(we also do that to hide a lot of complexity, e.g. file conversion,
directory creation, preprocessing, etc.). We like to create high level
service (screen receptor X against library Z) and this generally
requires a lot of preparation on the server side.

If you like we also have embedded client for some workflow tools,
Vision (from mgltools), and Kepler.

I hope that helps.

Sincerely,
Luca


> Thanks,
>
>
>
> Jeff Allen
>
> Computational Biologist
>
> Quantitative Biomedical Research Center
>
> UT Southwestern Medical Center
>
> 214.648.4171 - NC8.512B
>
> Jef...@UT...
>
>
>
>
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