[Biojava-l] Local binary execution
Francois Pepin
fpepin at cs.mcgill.ca
Thu Jun 16 18:55:54 EDT 2005
Not quite true. I've been using linux x86_64 version of the sun jvm 1.5
for a while now.
I do agree that it's limited to windows, linux and solaris (32 and 64
bits for all). I don't know about other jvms.
I personally like 1.5 a lot, but I'm not sure if I'd force it on all
biojava users. Are you talking about core features, or just nifty add-
ons that can be selectively compiled using ant?
Francois
On Wed, 2005-15-06 at 09:36 +0800, Richard HOLLAND wrote:
> 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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> >
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