[Bioperl-l] Re: bioperl-run Codeml.pm fix_blength

[Albert Vilella]

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/
> 
> 
> 
> 
>