[Bioperl-l] Proposed bioperl module for local running of the NCBI standalone blastpackage

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Mon, 16 Oct 2000 19:33:56 +0100

First, based on the paper I don't really understand how you would deal with
a filling up a single multi-processor machine, but I haven't looked at the
sources yet. Second, 'Disperse' now seems to be restrictively licensed
(academics only), so it is out of the game (apart from the fact that I
don't understand this policy switch, I can tell you that I will be unable
to find any support internally for licensing such software while at the
same time pushing for permission to officially contribute free code to
free/open software -- can you really make money with this stuff? New
economy, I see.).


Aaron J Mackey <ajm6q@virginia.edu>@bioperl.org on 16.10.2000 14:38:02

Sent by:  bioperl-l-admin@bioperl.org

To:   Hilmar Lapp <hlapp@gmx.net>
cc:   schattner@alum.swarthmore.edu, bioperl-l@bioperl.org
Subject:  Re: [Bioperl-l] Proposed bioperl module for local running of the
      NCBI standalone blastpackage

On Mon, 16 Oct 2000, Hilmar Lapp wrote:

> Basically, I have one comment. It would be very helpful if such a module
> could also support running stand-alone BLASTs in parallel, e.g., if
> you've got a multi-processor machine. I know that the current NCBI BLAST
> supports multi-threading, but on well-equipped machines it often scales
> better to run multiple processes.

If there's enough interest, I would consider writing a bioperl wrapper for
'disperse' (which accomplishes batch parallelization via multiple
processes on potentially many different machines).  See:

Raphael Clifford and Aaron J. Mackey
Disperse: a simple and efficient approach to parallel database searching
Bioinformatics 2000 16: 564-565.


But even as it stands, if you wanted to obtain a stream of blast hits, you
could replace your system call to blast with a system call to disperse
(printing your query library to disperse's STDIN and reading it's STDOUT
via Open3 or somesuch).


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