--- makefile.orig	Thu Oct 11 01:54:00 2007
+++ makefile	Mon Dec  3 22:08:28 2007
@@ -1,5 +1,5 @@
 #uncomment and locally adapt next line to fix the full helpfile path name
-HELPFILENAME = -DHELPFILENAME=\"/usr/share/njplot/njplot.help\"
+HELPFILENAME = -DHELPFILENAME=\"$(LOCALBASE)/doc/njplot/njplot.help\"
 
 #comment out next line and uncomment next 2 to use the PDFLib Lite library 
 NO_PDF = -DNO_PDF
@@ -7,43 +7,45 @@
 #PDFLIB = -L$(PDF) -lpdf
 
 # c compiler and linker
-CC = gcc
+CC ?= gcc
 
 # Vibrant top directory
-VIBRANT = /banques0/ncbiJun04
+#VIBRANT = /banques0/ncbiJun04
+NCBIINC = $(LOCALBASE)/include/ncbi
+NCBILIB = $(LOCALBASE)/lib/ncbi
 
 
 # X11 include directory
-X11INCL = /usr/X11R6/include
+X11INCL = $(LOCALBASE)/include
 
 # motif library directory
-MOTIFLIB = /sw/lib
-MOTIFINCL = /sw/include
+#MOTIFLIB = /sw/lib
+#MOTIFINCL = /sw/include
 
 OBJECTS = njplot-vib.o
 OBJUNROOTED = unrooted-vib.o preptree.o
 
 
-CFLAGS  = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
-	-I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \
-	-Wimplicit-function-declaration -g
+CFLAGS  = -c -DWIN_MOTIF -Dunix -I$(NCBIINC) \
+	-I$(X11INCL) $(HELPFILENAME) $(NO_PDF) \
+	-Wimplicit-function-declaration
 	
 all: njplot  unrooted newicktops newicktotxt
 
 
 njplot : $(OBJECTS)
 	$(CC) -g -o njplot $(OBJECTS) \
-        -L$(VIBRANT)/lib \
+        -L$(NCBILIB) \
         -lvibrant -lncbi \
         $(PDFLIB)   \
-        -L$(MOTIFLIB) -lXm  \
-        -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
+        $(MOTIFLIB) \
+        -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm
         
 unrooted : $(OBJUNROOTED)
 	$(CC) -g -o unrooted $(OBJUNROOTED) \
-        -L$(VIBRANT)/lib -lvibrant -lncbi \
-        -L$(MOTIFLIB) -lXm \
-        -L/usr/X11R6/lib -lXmu -lXt -lX11  -lm
+        -L$(NCBILIB) -lvibrant -lncbi \
+        $(MOTIFLIB) \
+        -L$(LOCALBASE)/lib -lXmu -lXt -lX11  -lm
 
 newicktops: njplot-vib.c
 	$(CC) -DNO_GUI  -DNO_PDF -o $@ njplot-vib.c -lm