[Biojava-l] BLAST from Java

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Wed, 20 Feb 2002 09:21:59 +0000

Russell Smithies wrote:

> Has anyone had any luck running Blast locally from Java using Runtime.exec()
> and command array??

Yes ;-)  Running native executables via Runtime.exec() works fine for us - but
almost all the Runtime.exec() code we have written is designed to run under

Runtime.exec isn't exactly the most cross-platform aspect of Java, and it was
really conceived from a Unix-centric standpoint.  I can't comment on how well it
works under Windows - pretty much the only time we use Runtime.exec on Windows
is to do trivial things like launching web browsers from Java applications.

There is an interesting piece on Runtime.exec() at the link below:


This obviously relates to the Apple implementation, but you may well learn
something by reading it.

Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK