[Bioperl-l] StandAloneBlast

[Jason Stajich]

Cory -
You can specify the file just as you would on the cmd line running blast
-d PATH/TO/BLASTDB

so just specify the full path name of the db when specifying the db.

I would strongly encourage anyone wanting to see standaloneblast work
better for them to consider improving it - it currently does not have a
caretaker so no new improvements have gone in to it. It could certainly
use work to make sure it runs smoothly in lots of different situations.

Cory - would you want to make the improvements you suggest?



On Thu, 24 Oct 2002, Cory Spencer wrote:

>
> 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?)
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu