[Bioperl-l] Bio::Tools::Run prepare executions [was Re:bioperl-run Codeml.pm fix_blength]

[Albert Vilella]

Hi all,

Having thought about the previous thread on changing tempdir as a
settable value in Bio::Tools::Run::WrapperBase (Jason? should we?)...

...I wonder if it may be interesting (at least it would for me) to
have something like a "prepare" method for the execution wrappers in
Bio::Tools::Run.

What I'm looking for is a way to create the dirs corresponding to the
analysis one wants to conduct. The "prepare" method would create, but
not execute, the dir with the ready-to-run elements of the executables
according to the various input data files and parameters.

Right now, we have a "run" method that first prepares the elements
needed for the execution and then runs the program.

We also have container objects for program results in bioperl-live.

This "prepare" method might be useful for people wanting to generate
sets of analysis for further execution on queueing-based systems or
similar scheduled execution situations.

I agree that the sole "preparation" of an execution it might not fit
well with the idea of an execution wrapper as it is now in bioperl, so
any suggestions/comments/criticism are welcome.

Bests,

    Albert.



El dt 12 de 07 del 2005 a les 18:03 +0200, en/na Albert Vilella va
escriure: 
> El dt 12 de 07 del 2005 a les 11:47 -0400, en/na Jason Stajich va
> escriure:
> > Sounds good - would you just copy the dir to the users specified
> > outdir?
> 
> yes
> 
> >    Another way to go is make tempdir a settable value (see
> > Bio::Tools::Run::WrapperBase -- in bioperl-live repository) - but
> > this may not be as clear on how to use it?
> 
> well, it is not as direct as the other way but maybe it is cleaner in
> the sense that will directly run the analysis on $tempdir and no extra
> cp or mv would be needed...
> 
>    Albert.
> 
> > 
> > 
> > -jason
> > On Jul 12, 2005, at 11:40 AM, Albert Vilella wrote:
> > 
> > > El dt 12 de 07 del 2005 a les 11:28 -0400, en/na Jason Stajich va
> > > escriure:
> > > 
> > > > sure - fix away.
> > > > 
> > > 
> > > 
> > > done.
> > > 
> > > 
> > > Also, in my pipeline it would be interesting to call Codeml.pm via
> > > bioperl keeping the tempfiles in a specified directory:
> > > 
> > > 
> > > I understand that save_tempfiles will save the generated tempfiles
> > > in
> > > the temp directory, the dir will remain in $tempdir.
> > > An $outdir could be specified so that the codeml run is saved where
> > > the
> > > user specifies.
> > > 
> > > 
> > > What do you think?
> > > 
> > > 
> > >     Albert.
> > > 
> > > 
> > > 
> > > 
> > > 
> > 
> > --
> > 
> > Jason Stajich
> > 
> > jason.stajich at duke.edu
> > 
> > http://www.duke.edu/~jes12/
> > 
> > 
> > 
> > 
> >