[Bioperl-l] Remote BLAST support discussion
cjfields at uiuc.edu
Fri Feb 10 12:45:32 EST 2006
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> Jason Stajich
> Sent: Friday, February 10, 2006 11:15 AM
> To: Paul.Boutros at utoronto.ca
> Cc: BioPerl Mailing List
> Subject: [Bioperl-l] Remote BLAST support discussion
> Paul -
> The reason for suggesting a change has to do with the
> instability of the CGI interface/format of the returned data,
> the text format is not a stable format from the webserver
> which reportedly will cease to be reliably parsed. Yes we
> can keep hacking the blast parser code to handle this, but
> the bioperl release cycle is certainly not tied to the NCBI
> blast release cycle so I find it unsatisfying to know that we
> are going to have broken code when they change the output
> formats (but not know when).
> Mostly I think we need to try and support something that will
> "ALWAYS" work so that individuals setting up webservices
> which rely on remote blast functionality. In theory,
> netblast/blastcl3 should always work since NCBI has to update
> the exe when they change their server setup.
> In terms of the web-based queues - I think the best change we
> can make is have the XML be the preferred retrieval method.
> I also see value in providing a wrapper for netblast since it
> should look an awful lot like running blast locally.
> Ideally I'd like to see a more extensible system, something
> like (and please feel free to come up with better names for
> the modules!):
> --> StandAlone (support for both WU-BLAST and NCBI-> BLAST
local binaries and MPI-BLAST too if simple)
> --> RemoteNCBI (currently the RemoteBlast server)
> --> RemoteEBISOAP (EBI has a nice SOAP interface that works
quite well, but may not provide all the same databases as what people expect
> --> RemoteNetBlast (blastcl3 or netblast local executable)
> (other things that people want)
Sounds good to me. I think any wrapper for netblast could most easily be
based on StandAloneBlast; the parameters look pretty much identical, though
it'll probably need a little configuring as a quick text search through
StandAloneBlast didn't show any 'xml' tags. Roger seemed to agree on this.
> [note: If these ideas are appealing or not, someone should
> archive the discussions and discussions on the wiki page so
> we can rely less on people searching the mailing archives for
> how a decision was made. Perhaps Roger can do this sort of
> editing in addition to the planning for support of this module].
> On Feb 7, 2006, at 8:38 PM, Paul Boutros wrote:
> > Hi Roger,
> > I would definitely prefer a fully Perl-based implementation. For
> > starters, I have not been successful in compiling the Toolkit that
> > contains netblast for some platforms (e.g.
> > AIX 5.2 w/gcc 4.0).
> > I haven't been following the discussion: is there some compelling
> > reason to prefer a netblast-based system that's come up
> recently? I'm
> > guessing that adding a new non-perl dependency would only
> be done if
> > there was considerable justification for this type of
> change, but I'm
> > not clear from your message what that justification is.
> > Paul
> > ------------------------------
> > Message: 12
> > Date: Mon, 6 Feb 2006 20:46:44 -0600
> > From: "Roger Hall" <rahall2 at ualr.edu>
> > Subject: [Bioperl-l] RemoteBlast users - potentially major changes -
> > please reply
> > To: <bioperl-l at lists.open-bio.org>
> > Message-ID: <002001c62b90$bb9dbe00$4301a8c0 at LIBERAL>
> > Content-Type: text/plain; charset="us-ascii"
> > To everyone who uses RemoteBlast.pm:
> > Would anyone object to RemoteBlast being rewritten in a way that
> > requires NCBI's blastcl3 executable?
> > Binary downloads of blastcl3 (column "netblast") are available for
> > numerous platforms at: http://ncbi.nih.gov/BLAST/download.shtml
> > Does anyone require or desire a "pure perl" implementation? If so,
> > please explain the advantage you see with such an implementation.
> > Thanks!
> > Roger Hall
> > Technical Director
> > MidSouth Bioinformatics Center
> > University of Arkansas at Little Rock
> > (501) 569-8074
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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> Jason Stajich
> Duke University
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
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