[Bioperl-l] Bio::Tools::Run::TribeMCL

[Jason Stajich]

On Sep 9, 2005, at 10:41 AM, Albert Vilella wrote:

>> How
>> can I make it put the output in the directory the program was  
>> called -
>> is there a flag I can add to the @params ??
>>
>
> Hi all,
>
> Jason and myself were considering to convert the tempdir method in
> Bio::Tools::Run::WrapperBase in a setter/getter, so that instead of
> getting a random tempdir, one could set the tempdir to a defined  
> value:
>
> Something like:
>
> sub tempdir{
>    my ($self) = @_;
>
> ## Add the setter part here
>     return $self->{'_tmpdir'} = shift if @_;
> ##
>    unless( $self->{'_tmpdir'} ) {
>        $self->{'_tmpdir'} = $self->io->tempdir(CLEANUP => !
> $self->save_tempfiles );
>    }
>    unless( -d $self->{'_tmpdir'} ) {
>        mkdir($self->{'_tmpdir'},0777);
>    }
>    $self->{'_tmpdir'};
> }
>
> Jason: How do you want the CLEANUP part to behave if the tempdir is
> setted? The same way as save_tempfiles?

[oops this got buried in the mail...]

Hmm - I think if the user requests a specific tempdir then we are not  
obligated to clean it up.  That would be my feeling.  Do the folks  
who want this functionality have an opinion about it?

It will be a bit of a pain to go back and try and cleanup a user  
specified dir as this is currently handled by the tempdir function  
already,  so I think a good reason has to be made for when a user  
wants to specify a particular tempdir but ALSO wants the tempfiles  
cleaned up afterwards.

In general  Albert - this sound good  - please feel free to make the  
changes at least about the setting of tempfile.

If it is just a simple added feature we can sneak it into bioperl  
1.5.1 this week before the release.

>
> Bests,
>
>     Albert.
>
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>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/