[Bioperl-l] StandAloneBlast

[Cory Spencer]

Is it currently possible to run the Bio::Tools::Run::StandAloneBlast
module *without* having to set the BLASTDATADIR environment variable?  I
currently have blast database files in several directories, and unless I'm
missing something, it's not possible to have multiple instances of
StandAloneBlast in the same program referencing different data
directories.  The BLASTDATADIR environment variable doesn't seem to be a
requirement of any particular BLAST implementation, rather a requirement
of the module itself.  It should be possible (and from my
viewpoint, preferable) instead to add -blastdatadir/-blastdir options to
the  constructor to facilitate this (while at the same time, defaulting to
the environment variable values if not provided to maintain backwards
compatability.)

Were there any particular reasons it was implemented this way?  (And have
I managed to overlook something that I should be aware of?)

-- 
Cory Spencer <cspencer@sfu.ca>         Phone: (604) 291-4206
Bioinformatics Application Developer   Fax: (604) 291-5583
Brinkman Lab, Simon Fraser University  Web: www.pathogenomics.sfu.ca/brinkman