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Accessing NCBI toolkit and HMMER with Java

Don Gilbert gilbertd at bio.indiana.edu
Wed Mar 6 15:37:35 EST 2002

A while back I was looking at trying to get EMBOSS package built
into a JNI library, but found it too non-reentrant to work that way.
The ones you are interested may work well.  This test of mine
never did fine-grained calls into the software,just an entry
from JNI into program main() such as
package emboss;
public class equicktandem extends iubio.jni.ChildAppJNI {
 public native int jnirun( String args[], String stdin, String stdout, String stderr);

There is a collection
of java source I've written for running bioinformatics command line
programs using System.exec() calls. BLAST, EMBOSS and others are
easy to run this way.  This source is in progress, cut from old
SeqPup with newer grid (globus COG toolkit) methods pasted in.
It includes for running command-line apps where input data, outputs
and command options can be described in command files (now XML,
along lines of Pise (Catherine Letondol's web interface).  The
programs can be locally installed or on remote, grid-aware servers.
Find docs at http://iubio.bio.indiana.edu/grid/
and source links there-in.

-- Don

In article <3c84eee1.491673118 at news.west.cox.net>,  <wparkman at cox.net> wrote:
>I am putting Java JNI wrappers on the C code in the  NCBI Software
>Development Toolkit ( ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools ) and
>also on the C code in HMMER ( http://hmmer.wustl.edu ) so that I can
>call methods in these programs from  Java classes.
>Has anyone done this already?  Are there packages available for
>invoking Blast or HMMER from Java?

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu

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