The obvious choice then is to redefine the classpath in the manifest
file or have a ant script to create the jar (biojava is in the lib
directory) :
<target name="myjar" >
<jar jarfile="myJar.jar" index="false" >
<fileset dir="myClassesDirectory"/>
<manifest>
<attribute name="Built-By" value="${env.USER}"/>
<attribute name="Class-Path" value="lib/biojava.jar"/>
<attribute name="Main-Class" value="myMainClass"/>
<attribute name="Sealed" value="true"/>
</manifest>
</jar>
</target>
hmmmm...
does this help or what ?
Al.
On Fri, 2005-02-11 at 14:30, Michael Heuer wrote:
> Hello Alex,
>
> Combining the java command line arguments -cp and -jar will not work as
> you expect -- the -jar argument overrides the CLASSPATH.
>
> "When you use this option, the JAR file is the source of all user
> classes, and other user class path settings are ignored."
>
> > http://java.sun.com/j2se/1.5.0/docs/tooldocs/solaris/java.html#options
>
> michael
>
>
> On Fri, 11 Feb 2005, Alexandre Dionne-Laporte wrote:
>
> > include the full path of the biojava archive in the definition of your
> > classpath:
> >
> > #java -cp
> > /uufs/inscc.utah.edu/common/home/ahammer/ext/xerces.jar:/uufs/inscc.utah.edu/common/home/ahammer/ext/biojava.jar
> > -jar MotifSearch.jar
> >
> > Alex.
> >
> > On Fri, 2005-02-11 at 14:02, Andy Hammer wrote:
> > > I think I am on the same page as everyone here.
> > > But I still get:
> > > >java -cp xerces.jar:biojava.jar -jar MotifSearch.jar
> > > Exception in thread "main"
> > > java.lang.NoClassDefFoundError:
> > > org/biojava/bio/BioException
> > >
> > > More info:
> > > [EMAIL PROTECTED]:~/ext> pwd
> > > /uufs/inscc.utah.edu/common/home/ahammer/ext
> > > [EMAIL PROTECTED]:~/ext>
> > > [EMAIL PROTECTED]:~/ext> echo $CLASSPATH
> > > .:/uufs/inscc.utah.edu/common/home/ahammer/ext/
> > > [EMAIL PROTECTED]:~/ext>
> > > [EMAIL PROTECTED]:~/ext> ls -l
> > > total 4772
> > > -rw-r--r-- 1 ahammer gestelan 2674782 2003-10-15
> > > 10:37 biojava.jar
> > > -rw-r--r-- 1 ahammer gestelan 93463 2003-10-07
> > > 17:59 bytecode.jar
> > > -rw-r--r-- 1 ahammer gestelan 30117 2003-10-07
> > > 17:59 commons-cli.jar
> > > -rw-r--r-- 1 ahammer gestelan 145563 2003-10-15
> > > 10:04 grammars.jar
> > > -rw-r--r-- 1 ahammer gestelan 46056 2003-10-07
> > > 17:59 htmlparser.jar
> > > -rw-r--r-- 1 ahammer gestelan 50962 2005-02-10
> > > 11:38 MotifSearch.jar
> > > -rw-r--r-- 1 ahammer gestelan 1808885 2005-02-11
> > > 11:55 xerces.jar
> > > [EMAIL PROTECTED]:~/ext>
> > >
> > > I don't understard why this doesn't work. It works
> > > fine on a windows box. It makes me think it wouldn't
> > > work even if I had access to the jre/ext directory.
> > >
> > > Andy
> > >
> > >
> > >
> > > __________________________________
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> > > _______________________________________________
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> > > http://biojava.org/mailman/listinfo/biojava-l
> > _______________________________________________
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> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
>
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