[kepler-users] Perl actor for Kepler 2.3

[Matt Jones]

Josep,

If you already created the actor for Kepler 1.0, then for the most part it
will be able to work in 2.0 with some repackaging and minor redesign.  The
actor API is still basically the same, but the way we package actors in
KARs and modules has changed.  A perl actor would be generally incredibly
useful, so we would be happy to help maintain it if you contributed the
actor to the project.  Probably the way to start that would be to create a
Kepler module for the perl actor.  To accomodate that, I could create a
module to hold such an actor.  If you get a development account, would you
contribute your work there?

In terms of approach, the easiest approach is to simply invoke perl in an
external shell process in Kepler (using the same approach used in the
commandline actors), and use the actor to properly arrange input and output
to that external process.  The advantage here is simplicity, but has the
cost of limited scalability, as the process overhead of creating many
different shell processes for each actor invocation can be overwhelming for
some workflows.  But, it has worked reasonably well for other external
languages like R, so it may meet your needs here.  A more sophisticated
approach would be to build a perl processing engine using Proc::Daemon that
can accept perl code and execute each request in its own sandbox without
restarting the engine.  This would be similar to the approach that RServer
takes to execute R code, and would avoid some of the invocation overhead of
creating new shell processes.  But of course it would be harder to do as
well.

Matt

On Thu, Jan 26, 2012 at 8:20 AM, Christopher Brooks
<cxh at eecs.berkeley.edu>wrote:

> Dear Joseph M.
> The hello world actor tutorial would be the best place to start.
> I don't know of an easier way to add a Kepler 1.0 Perl actor to Kepler 2.x
>
> _Christopher
>
>
> On 1/26/12 1:25 AM, Josep Maria Campanera Alsina wrote:
>
>> Dear users,
>> How is possible to run perl code like R or python codes do with the
>> corresponding actors? I now, It has been a recurrent question from me,
>> but perl scripting is quite common in my area of bioinformatics. So it
>> would be extremely useful to have a perl actor embbeded by default in
>> Kepler. I programmed a custom perl actor for kepler 1.0 but now it is
>> out of date! It is a way to update this actor to kepler 2.3 without
>> doing the following tutorial?
>>
>> https://kepler-project.org/**developers/teams/build/**
>> documentation/developing-a-**hello-world-actor-using-the-**
>> kepler-build-system-and-**eclipse<https://kepler-project.org/developers/teams/build/documentation/developing-a-hello-world-actor-using-the-kepler-build-system-and-eclipse>
>>
>> Thank you!
>>
>> Josep M.,
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>>
>
> --
> Christopher Brooks, PMP                       University of California
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