[Biojava-l] Intsall Problems Update

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Sun Feb 29 20:22:56 EST 2004

Hi -

The biojava-live and build.xml files are specific to the CVS distribution 
which is the development version. If you are happy to use biojava 1.3.1 
(or earlier) you just need the precompiled jars on your classpath. You 
don't really need the source files but it is nice to have them so you can 
look at the code.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910

"Orion Hunter" <orion2480 at hotmail.com>
Sent by: biojava-l-bounces at portal.open-bio.org
02/29/2004 02:10 AM

        To:     biojava-l at biojava.org, smh1008 at cus.cam.ac.uk
        Subject:        Re: [Biojava-l] Intsall Problems Update

Thanks for the response.  I got everything working, but it took a little 

First off, I never found the biojava-live directory.  I know I had ANT 
installed correctly, because it worked from the command line... but I 
found the biojava-live nor the build.xml that ant looks for.

So, I d/l the jars themselves.  However, in order to get everything to 
I had to include in my classpath the location of the packages (basically, 
had to include /home/user/biojava/main in my class path, because this is 
root of where the pakcage structure is located), in addition to the normal 

classpath of the JARS.

The second thing I had to do was go in and individually compile many of 
.java files in the packages.  Javac'ing the demo files for whatever reason 

did not do this (and I tried several times, recompiling the demofiles to 
if that would result in the necessary class files from the packages).

Anyway, in the end I got it to work.  Just took a little extra work.


>From: David Huen <smh1008 at cus.cam.ac.uk>
>Reply-To: smh1008 at cus.cam.ac.uk
>To: "Orion Hunter" <orion2480 at hotmail.com>, biojava-l at biojava.org
>Subject: Re: [Biojava-l] Intsall Problems Update
>Date: Sat, 28 Feb 2004 12:50:25 +0000
>On Friday 27 Feb 2004 9:36 pm, Orion Hunter wrote:
> > So, I added
> >
> > /home/user/biojava/main to my classpath, since org.biojava.* sits in 
> > directory (maybe this should be mentioned in the getting started 
> > I got rid of all my compile errors, but am encountering runtime errors
> > now:
> >
> > /home/user/biojava/demos>$ java seq.TestEmbl seq/AL121903.embl
> > java.lang.NoClassDefFoundError:
> > org/biojava/bio/symbol/SimpleCrossProductAlphabet
> >         at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:54)
> > rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
> >         at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:85)
> >         at seq.TestEmbl.main(TestEmbl.java:22)
> >
> > If I go into the directory of this package, there is no .class file 
> > this file (which is of course why I got this error).  HOwever, I 
> > figure out why there is no .class file.  I didn't get any compile 
> > but I would have thought this class file would have been compiled 
> > ANy suggestions?
> >
> >
> > From: "Orion Hunter" <orion2480 at hotmail.com>
> >
> > >To: biojava-l at biojava.org
> > >Subject: RE: [Biojava-l] Intsall Problems
> > >Date: Fri, 27 Feb 2004 21:11:47 +0000
> > >
> > >In case it makes a difference, I forgot to mention that I am using
> > >j2sdk1.5.0beta on an Intel based RedHat  9.1 machine.
> > >
> > >Matt
> > >
> > >p.s. Sorry for the "intsall" mispell
> > >
> > >>From: "Orion Hunter" <orion2480 at hotmail.com>
> > >>To: biojava-l at biojava.org
> > >>Subject: [Biojava-l] Intsall Problems
> > >>Date: Fri, 27 Feb 2004 20:39:21 +0000
> > >>
> > >>I am trying to install biojava.  I d/l biojava1.3.1, unziped and
> > >> untarred it.  I installed ANT, but I am confused.  It specifies to
> > >> execute ANT from the "biojava-live" directory, but I cannot find 
> > >> directory, nor any build.xml files anywhere.
> > >>
> > >>So, then I try to download the jar file.  I download all three 
> > >>files (biojava.jar, bytecode.jar, and xerces.jar).  I add them to my
> > >>classpath (and have confirmed that the classpath is correct and is
> > >>remembered by the machine in my env).
> > >>
> > >>So, with a set of jars, I decided to try out the demo.  Following 
> > >>instructions on the website (in the "getting started" section), I cd 

> > >>the demos/, and type the following:
> > >>
> > >>/home/user/biojava/>javac seq/TestEmbl.java
> > >>
> > >>I get a whole slew of errors, of which all look like they have to do
> > >> with the fact that it can't find the packages in org.biojava.bio, 
> > >>  Now, I can see this package structure in
> > >>
> > >>/home/user/biojava/main/org/biojava/bio, etc.
> > >>
> > >>And I was trying to execute from /home/user/biojava/demos
> > >>
> > >>So, why can't it find the packages?  I'm not new to java, but it's 
> > >> a long time since I've had to deal with packages, and I can't 
> > >> how to make biojava see where the packages are located.  Any
> > >> suggestions?
> > >>
>OK, I will go thru' the steps necessary to do a compile and installing 
>jars that result from the compile.
>1) install ant
>You mentioned you have done this.  Do ensure that the ant bin/ directory 
>in PATH so typing "ant" will execute ant.
>2) compile the BJ source tree.
>cd <wherever the the biojava-live directory is>
>3) setting up the CLASSPATH
>Java relies on the CLASSPATH to find classes it needs.  You have to set 
>CLASSPATH to include the jars that biojava depends on as well as the jar 
>which biojava resides.
>running ant creates the biojava.jar in the biojava-live/ant-build 
>If you wish to use that jar, you must put it into your CLASSPATH.  I
>usually set up my CLASSPATH in .bash_profile at login.
>If you are just d/ling the precompiled biojava-1.3.jar, you still need to
>put it into your CLASSPATH or java will nto find the classes it wants and
>give you the error messages your are reading.
>At this stage, things should just work.
>David Huen

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