[Bioperl-l] Re: tempfile creation and Bio::Tools::Run

Ewan Birney birney@ebi.ac.uk
Sun, 17 Dec 2000 19:23:59 +0000 (GMT)

On Sun, 17 Dec 2000, Jason Stajich wrote:

> Since File::Temp seems to be causing problems, does it make more sense to
> migrate tempfile creation to RootI and use File::Temp if it exists and
> fallback on a more simplified method we write in bioperl if it doesn't?

sounds good to me.

> We definitely needed to go to tempfile creation for StandAloneBlast rather
> than hardcoded tmp1.fa as it is concievable to have >1 blast process running
> in the same directory.  Will need to do the same for the ClustalW and
> TCoffee running as well.


> As Hilmar has suggested, how about moving modules that run external
> applications to Bio::Tools::Run - while things that are typically parsing
> output from programs can stay in Bio::Tools.

Also sounds good.

I was going to suggest to wait for Hilmar to say ok, but as he suggested
it and you and I are ok with this, then I think it passes the "main
developers" litmus test. Go for it.

> -Jason

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420