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

[Jason Stajich]

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?

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.

-Jason