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

[Peter Schattner]

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. So, the idea is then that I can pass an
> array of Seq objects and these will be run in parallel, returning an
> array of BPlite or Blast.pm objects. At the low-level, there may be a
> memory issue if the array is a few hundreds or thousands seqs long (which
> it is for us). So, instead of returning a full array of result objects,
> one may consider a callback invoked for each finished report.


This all sounds fine to me.  However, since my experience with
parallel-processing and multi-threading (especially from within Perl) is
very close to zero, I am probably not the best person to be
incorporating this capability into the StandAloneBlast module.  On the
other hand, if it’s just a matter of leaving in some "hooks" so that it
is easier to add parallel -processing / multi-threading capability in
the future, let me know what needs to be done and I’ll make sure to
leave such hooks available in the module.

Peter