[Biojava-l] library for running blast and formatdb

[Wiepert, Mathieu]

It would be good if a command could be described somehow (XML file?), and the interface could query that to find commands, limits, parameter acceptable values, location of programs maybe?  Short of the commands being self-describing, and you knew where they all were, that might not be so bad?  Simple website wrappers could then be written around them, common look and feel for all commands, etc...  I'd swear I had seen something like this somewhere, generically implemented (thought it was for unix commands on a machine).  Something like this would allow new programs and scripts to plug in rather easily.  Hmmm, I have strayed off topic, sorry.

-Mat

> -----Original Message-----
> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> Sent: Monday, January 13, 2003 2:08 PM
> To: Patrick McConnell
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] library for running blast and formatdb
> 
> 
> One thing sorely missing from BioJava is the ability to launch and
> capture the results of common bioinformatics programs. I know 
> Java isn't
> the best at this but it's not that bad. It's also needed if 
> you want to
> develop pipeline type applications.
> 
> Would it be possible to get some kind of over-arching interface based
> API so that services can be made available with similar interfaces.
> 
> Possibly a Service or Program interface a Paramater list or map, some
> kind of result stream?
> 
> Just my $0.02
> 
> - Mark
> 
> > -----Original Message-----
> > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu] 
> > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > To: biojava-l@biojava.org
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > 
> > 
> > >I suppose it's a matter of another external dependency vs. 
> > reinvented 
> > >utility code in biojava . . .  Would it make sense to merge 
> > the better 
> > >qualities of the two?
> > 
> > The CLI project looks like it is quite flexible and robust.  
> > But, with this, it is somewhat complex.  This is in contrast 
> > to the simplicity of creating parameters via reflection.  I 
> > think that these two methods could be effectively combined so 
> > that we gain the simplicty of reflection with the flexibility 
> > of CLI.  The base parameters class can use CLI to build its 
> > parameters.  As an option, it can build CLI options via 
> > reflection for simplicity.  When users extend the base class, 
> > they can utilize the flexibility of CLI if they need it, 
> > otherwise they can use reflection for a quick and dirty 
> > parameter parsing.  The base class could even extend the 
> > Options class, so we are really working with a hybrid of the 
> > two.  What does everyone think?
> > 
> > -Patrick
> > 
> > 
> > 
> > 
> > 
> > 
> > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on 
> > 01/10/2003 05:18:52 PM
> > 
> > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> > 
> > 
> > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > cc:    biojava-l@biojava.org
> > 
> > Subject:    Re: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> > 
> > > In the process, I developed some useful and flexible base 
> > classes for 
> > > formatting parameters and running programs.  Parameters are 
> > > automatically converted to an argument array via reflection and 
> > > reading of standard out and standard error in separate threads is 
> > > handled automatically.
> > 
> > The base classes are nice, but I prefer the design of
> > 
> > > http://jakarta.apache.org/commons/cli
> > 
> > a lot better for handling parameters.
> > 
> > I suppose it's a matter of another external dependency vs. 
> > reinvented utility code in biojava . . .  Would it make sense 
> > to merge the better qualities of the two?
> > 
> > I also have a few simple classes for oneoff scripts with 
> > command line & logging facade support that I use all the time, see
> > 
> > > http://www.shore.net/~heuermh/oneoff.tar.gz
> > 
> > but they don't have any extra support for external programs.
> > 
> >    michael
> > 
> > >
> > > Check it out if you are interested: 
> > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full 
> > > source, javadocs, and binary class files are available.  
> > Also, if this 
> > > seems appropriate for BioJava, I have no problem donating 
> it to the 
> > > cause.  I think that at least the base classes, or some 
> > modification 
> > > of them, would be useful to others.
> > >
> > > Please email me with suggestions/comments,
> > >
> > > -Patrick McConnell
> > > Duke Bioinformatics Shared Resource
> > > mccon012@mc.duke.edu
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
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