[Biojava-l] library for running blast and formatdb
Brian Gilman
gilmanb@genome.wi.mit.edu
Mon, 13 Jan 2003 15:38:01 -0500
On 1/13/03 3:19 PM, "Wiepert, Mathieu" <Wiepert.Mathieu@mayo.edu> wrote:
This functionality exists in the OmniGene Analysis Engine! (OAE). I could
help you get up and running if you are interested.
-B
> 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
>>>>
>>>>
>>>> _______________________________________________
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>>>> http://biojava.org/mailman/listinfo/biojava-l
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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--
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902