Bioperl: Final pre release

[Steve Chervitz]

Jonathan,

The latest prerelease has been updated to deal with the current NCBI
blast server, but it's not the ideal solution. It's a two-step process
of first entering the blast jobs in the queue (using
run_blast_remote.pl), and then retrieving them using a separate script
(retrieve_blast.pl). It isn't geared for batch processing and could
defininitely be more user-friendly.

Bioperl is open to your suggestions here, but in general, we don't want 
to create too many dependencies on external software, to keep bioperl
as self-contained as possible. In the case of running remote blasts
however, using external software is more reasonable since we are
accessing an external resource.

So I'm open to your suggestion here. I'm not familiar with the
blastcl3 client. Tell me more.

Steve
sac@neomorphic.com

Jonathan Epstein writes:
 > I'm a bit afraid to ask this, but here goes.  Does this current prerelease
 > version interoperate with the current NCBI blast server?  Some previous
 > versions were incompatible after NCBI changed its Web submission format.
 > 
 > Have the bioperl developers consider using the blastcl3 client software as an
 > interface to NCBI blast?  This should be a much more stable interface.  If it
 > makes sense to do so, then I will take a look at it.  I will probably do this
 > sooner rather than later if the current blast bioperl software is broken ;-)
 > 
 > - Jonathan
 > 
 > At 01:22 PM 3/23/00 , Ewan Birney wrote:
 > >
 > >I have put in the 06 branch. This means that we have now decide on
 > >the feature set, functionality and general code to work for the new
 > >0.6 release of bioperl. 
 > >
 > >It is *very* important that people who use bioperl heavily that they
 > >try to pick this release up and test it, ideally in place of their
 > >exisiting bioperl. It *should* be backwardly compatible (you will
 > >get warnings when you use deprecated methods). There are so many
 > >new aspects to bioperl, including better performance and richer
 > >object definitions that it is undoubtedly worth upgrading.
 > >
 > >
 > >The release is at
 > >
 > >ftp://bio.perl.org/pub/birney/bioperl-06pre3.tar.gz
 > >
 > >It is a standard CPAN module, so installation should be trivial.
 > >
 > >
 > >
 > >I'd like to publically thank many people who contributed to this
 > >release and in particular the new comers. They include:
 > >
 > >  James   Gilbert
 > >  Heikki  Lehväslaiho
 > >  Jason   Stajich
 > >  Elia    Stupka
 > >  Lincoln Stein
 > >  Peter   Schattner
 > >  Michele Clamp
 > >  Kate    Linder
 > >  
 > >Please - I am not sure that I have everyone who has committed stuff over
 > >the last 6 months, so if you know you have contributed, whether in code,
 > >testing, documentation or design, please speak up. (yes - we need to start
 > >a contributor's list).
 > >
 > >Just to mention, bioperl is not possible without the continued work
 > >of 
 > >
 > >  Steve Chervitz
 > >
 > >and in particular, a big thank you to
 > >
 > >  Chris Dadigdan
 > >
 > >who provides system administration to the entire bio* set of sites
 > >
 > >
 > >
 > >
 > >Anyway - go get it - go test it! Expect the full release next week with a
 > >revamped web site.
 > >
 > >
 > >
 > >
 > >
 > >
 > >
 > >
 > >-----------------------------------------------------------------
 > >Ewan Birney. Mobile: +44 (0)7970 151230
 > ><birney@ebi.ac.uk>
 > >-----------------------------------------------------------------
 > >
 > >
 > >
 > >
 > >
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 > 
 > 
 > Jonathan Epstein                                Jonathan_Epstein@nih.gov
 > Unit on Biologic Computation                    (301)402-4563
 > Office of the Scientific Director               Bldg 31, Room 2A31
 > Nat. Inst. of Child Health & Human Development  31 Center Drive
 > National Institutes of Health                   Bethesda, MD 20892
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