[03/18/2002:  I just noticed this old NOTES file, which was last updated
Nov 6, 2000!  I'm going to try to update it, but it won't all happen
right away, so keep in mind that the information here is not all up to
date!  --NH]

Checking out apollo from SourceForge CVS:
=========================================
setenv CVS_RSH ssh
cvs -z3 -d:ext:USERNAME@cvs.gmod.sourceforge.net:/cvsroot/gmod co apollo

apollo config file
==================
To start up, Apollo needs to read a config file, which is usually called
apollo.cfg (Ensembl's is called ensembl.cfg).

apollo looks for apollo.cfg in $HOME/.apollo/apollo.cfg.  If there isn't
one there, it uses the one in APOLLO_ROOT/data.

Setting which Java apollo uses
==============================
If you have many versions of Java on your system and you want bin/apollo to use a certain version,
you can change the JavaPath line in your apollo.cfg:

On Solaris, java is /bin/java, thus JavaPath is just "/"
On Linux, java is /usr/lib/java/bin/java, thus JavaPath is /usr/lib/java
On Mac OS X, java is /usr/bin/java, thus JavaPath is /usr

It would probably make more sense to have JavaPath be the actual path to java, e.g.
/usr/lib/java/bin/java, but that would make this apollo.cfg incompatible with
the Berkeley version.

Quick start
===========
To run apollo with the jar file supplied, run bin/apollo (which is in APOLLO_ROOT)

To run on the example Sanger gff file (if you're in APOLLO_ROOT)
  ./bin/apollo -f test ./data/test1.gff

To run on the Berkeley GAME XML example file:
  ./bin/apollo -x data/example.xml

Running without remaking the jar
================================
If you're a developer and want to run apollo directly from the class files without
having to constantly remake the jar, use the "-s" argument to the bin/apollo script:
       bin/apollo -s -x data/example.xml

Compiling Apollo Java code
==========================
Apollo should compile with Java 1.3 and 1.4.

There is a Makefile in src/java. To make java progs (including
compiling the IDL):
setenv APOLLO_ROOT /dir/where/you/have/apollo/installed
cd src/java
make
