[Bioperl-l] migrated modules to a run dir

Jason Stajich jason@chg.mc.duke.edu
Sun, 17 Dec 2000 16:46:02 -0500 (EST)

Migrated the Bio::Tools::StandAloneBlast.pm, Bio::Tools::Alignment::* to

I have also added the capability of tempfile and tempdir creation from
Bio::Root::RootI, all modules that use tempfiles should probably use these
methods as it handles the absence of File::Temp.  Currently the code
automatically deletes temporary files upon destruction of the object that
called tempfile.

Unfortunately the output files created by Bio::Tools::Run::Alignment::*
produce .dnd dendogram files which are created in CWD not in the dir where
the temporary files are located (/tmp).  So my code to remove them is
not looking in the right place...  I'll add some better code to allow
users to specify whether or not to delete these files (in case you want to
use the dendogram files).  Will removed them for sure when created by
the tests.  But is it more correct for them to be put in
the current dir or where the sequences files are located.  I can imagine
arguments for both sides.

Can't do any of this till Monday though, so user be warned when you run
make test on the main trunk.

Jason Stajich
Center for Human Genetics
Duke University Medical Center