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

[Jason Stajich]

Sounds good - would you just copy the dir to the users specified outdir?
    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?

-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/