[Biojava-l] a newbie interested in trying biojava

[Thomas Down]

On Thu, Feb 21, 2002 at 07:44:59AM +0530, mandavya wrote:
> hi all,
>       I am a biologist developing interest in bioinformatics.
>       I have downloaded the following jar files from the biojava site.
> 1. biojava-1.11
> 2. biojava-20010702
> 3. biojava-20010920
> 4. biojava-20020111
> 5. bytecode-0.90
> 6. jakarta-regexp
> 7. xerces
> 8. xml
>           I have my jdk1.3/bin in C drive .
> 
> I tried to follow the documentation for installing these packages. But i failed. Please tell me where to copy these jars, before
> that check whether the downloaded jars are adequate and up-to-date.


Okay, it looks like you've downloaded several different
versions of BioJava, all of them a bit old now (the releases
with an 8-digit number are snapshot releases.  We should
probably delete some of the older ones.

I'd recommend you use the recent BioJava 1.20 release
for now.  The other things you'll require are:

   xerces.jar (XML parser)
   jakarta-regexp.jar
   bytecode-0.90.jar

Strictly speaking, BioJava doesn't need to be `installed'.
You can place the .jar files anywhere on your system,
then set up the CLASSPATH environment variable to tell your
Java runtime where to find them:

  set CLASSPATH C:\biojava\biojava-1.20.jar;C:\biojava\xerces.jar;C:\biojava\bytecode.jar;.


Then take a look at the tutorial:

  http://www.biojava.org/tutorials/index.html

And try compiling a simple example program (try GCContent,
from the first chapter of the tutorial).


Let me know if you have any more trouble,

    Thomas.