Pick some directory MAUVEDIR in which to put application jars and such.  This 
should be accessible via the path MAUVEPATH.

I.  Set up files. (Do this for every deployment).

	1.  Set the properties "asap.dir" to MAUVEDIR and "asap.codebase" to MAUVEPATH
		in build.xml.  Then run the target "deployASAP".  This will copy over the old
		version, if present.  *If additional external dependencies are added to the
		project, then use the "signextjars" target to add sign them.
		
		You will need to set the "key.password" property on the command line, using
		the option "-Dkey.password=<password>"
		
		This task updates a templatized JNLP file, so don't edit the JNLP file on the
		server, unless you want those changes to be lost in the future, which I doubt
		you would want.  It also copies required files, signs jars, all that nifty stuff.

II.  Update PHP code. (Only required on first setup)

	1.  Include the mauve-launching applet in basic_feature_info.php page:
	
		See lines 279-283 of ~pinfield/public_html/asap/basic_feature_info.  
		This should be copied entirely, changing the CODEBASE attribute to reflect
		the MAUVEPATH chosen.

	2.  Include link to open alignment at a particular location:

		See lines 160-163 of ~pinfield/public_html/asap/basic_feature_info.php for an
		example.  *The line beginning "$alignmentJarURL..." will need to be 
		adjusted to point to a meaningful jar file.*  Note the trailing "!/" in 
		the URL; this is very much required.

III.  Package alignments

	1.  Package alignment.
	
		See "makeMixedJar" target in build.xml for an example.  The file contents 
		are the alignment file and source files.  In the manifest, the following
		attributes are required:

		Mauve-Alignment: the name of the alignment file.
		Sequence-N-ID: the combination of ASAP genome id and location ID for the 
		Nth sequence, separated by an underscore.  

	2.  Put alignment where it belongs.
	
		Copy the resulting alignment file to wherever it needs to live to be
		accessible at URL generated for basic_feature_info link.
