--- ./Binary/makefile.orig	2008-06-12 16:00:19.000000000 -0300
+++ ./Binary/makefile	2008-06-12 16:00:43.000000000 -0300
@@ -11,10 +11,10 @@
 # copy of the SSAHA directory structure you should be able to make files
 # straight away.
 # 
-# SSAHA_TOP_DIR=$(SSAHA_DIR?$(SSAHA_DIR):$(PWD)/../)
+SSAHA_TOP_DIR=$(PWD)/../
 # Above is a nice idea, but syntax doesn't work for all versions of make
 # so must define CURRENT_SSAHA_VERSION, eg in your .cshrc file - TC 14.3.01
-SSAHA_TOP_DIR=$(CURRENT_SSAHA_VERSION)
+# SSAHA_TOP_DIR=$(CURRENT_SSAHA_VERSION)
 
 GLOBAL_DIR=${SSAHA_TOP_DIR}/Global
 SEQ_DIR=${SSAHA_TOP_DIR}/SequenceReader