[Biojava-l] Re: [Biojava-dev] Local binary execution

[Richard HOLLAND]

Linux supports Java 1.5 but only using the Sun JDK on ia32 and AMD
Opterons. Support for other architectures on Linux (such as ia64, PPC,
or Alpha) is restricted to specialist provisions from vendors such as HP
and the open source efforts such as Blackdown JDK. At a quick check, the
Alpha is only at 1.4.2 (from HP), likewise PPC (from IBM), whereas ia64
can run 1.5 apps using HP's JRE but no compiler yet exists for them.
There may also be some open source purists out there who object when
they can't use their favourite open source JDK any more...


Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> mark.schreiber at novartis.com
> Sent: Wednesday, June 15, 2005 9:09 AM
> To: Michael Barton
> Cc: biojava-l at open-bio.org; BioJava-dev
> Subject: [Biojava-l] Re: [Biojava-dev] Local binary execution
> 
> 
> We would normally not like to use a new JDK in biojava unless 
> it is well 
> supported on all the OS's people are using. Having said that 
> there are 
> several attractive features which would make it nice to use.
> 
> Is anyones current OS not supporting java 1.5?
> 
> - Mark 
> 
> 
> 
> 
> 
> Michael Barton <michael.barton1 at ncl.ac.uk>
> Sent by: biojava-dev-bounces at portal.open-bio.org
> 06/15/2005 02:26 AM
> 
>  
>         To:     BioJava-dev <biojava-dev at biojava.org>
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        Re: [Biojava-dev] Local binary execution
> 
> 
> I had a look at the post you were refering to. In terms of the ant
> support for local binary execution I think it is very similar to the
> newly implemented ProcessBuilder in Java 1.5.
> This class has a similar way way of adding command line arguments to
> that of ant <exec>.
> 
> The classes I'm suggesting have an enum of arguments specific to the
> application which may convienient for suppling different 
> switch/argument
> pairs, as it it means that only arguments for which the binary allows
> can be supplied.
> Any errors should therefore come from incorrent argument values rather
> than incorrect arguments. If that makes sense.
> In addition the class throws an exception if the essential arguments
> required to run the search are not supplied.
> 
> This means however that the classes are written in Java 1.5. 
> Would this
> be a problem?
> 
> 
> On Thu, 2005-06-09 at 11:54 -0400, Michael Heuer wrote:
> > Hello Michael,
> > 
> > Personally I think this kind of code might be better suited 
> in a more
> > general library, say in an Apache Jakarta Commons project 
> for example.
> > 
> > In fact, there was just a proposal to pull the exec code 
> out of ant into 
> a
> > separate self-contained library to the commonds-dev mailing list a 
> couple
> > of days ago:
> > 
> > > http://tinyurl.com/9culs
> > 
> > That said, this comes up quite frequently here, so perhaps 
> we should 
> just
> > bite the bullet and do it up right.
> > 
> >    michael
> > 
> > 
> > On Thu, 9 Jun 2005, Michael Barton wrote:
> > 
> > >
> > > Hi,
> > >
> > > I'm Bioinformatics MRes student at Newcastle. I've been 
> messing around
> > > with some java code to execute bioinformatics binaries. It was
> > > originally intended for blast but has also been extended 
> for genewise.
> > > It takes the hassle out of using process / process 
> builder a little 
> bit.
> > >
> > > Use goes along the lines of something like this
> > >
> > > //Search factory for creating searches
> > > SearchFactory<BlastSearch, BlastSearchFactory.Parameter> bsf;
> > > bsf = new BlastSearchFactory();
> > >
> > > //Paramterise with search specific variables
> > > bsf.setSearchBinaryLocation(test_data + "/blast/binary");
> > > 
> bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType,
> "blastn");
> > > bsf.setSearchParameter(BlastSearchFactory.Parameter.database,
> > >     test_data + "/blast/db/sargasso");
> > >
> > > //Create immutable search object which can be used to run mutiple
> > > searches on the same database
> > > Search<BlastSearchResult> blastSearch = bsf.getSearch();
> > >
> > > Simple search result object which returns inputstream
> > > SearchResult sr = blastSearch.execute(new File(test_data +
> > > "/blast/query/query"));
> > >
> > > InputStream is = sr.getResultStream();
> > >
> > > It's seems to work okay on linux, I haven't tested it on windows.
> > >
> > > There's a little bit of JavaDoc I started work on but 
> it's a little 
> bit
> > > messed up from where I've been changing things around.
> > >
> > > The source/jar/doc are all here. There's test cases too.
> > >
> > > http://www.students.ncl.ac.uk/michael.barton1/
> > >
> > > Mike
> > >
> > > _______________________________________________
> > > biojava-dev mailing list
> > > biojava-dev at biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-dev
> > >
> > 
> 
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