[Biojava-l] library for running blast and formatdb

Schreiber, Mark mark.schreiber@agresearch.co.nz
Tue, 14 Jan 2003 09:40:02 +1300


I notice there is a Object call AppBeanRunner that appears to make an
object from an XML file then instantiate it. Is it intended for the type
of activity below or something else?

- Mark

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu] 
> Sent: Tuesday, 14 January 2003 9:20 a.m.
> To: 'biojava-l@biojava.org'
> Subject: RE: [Biojava-l] library for running blast and formatdb
> 
> 
> 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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