--- Makefile.orig	Sat Oct  7 00:16:41 2000
+++ Makefile	Thu Dec 20 17:26:37 2001
@@ -19,10 +19,11 @@
 ## (this could be 'perl5' or otherwise on some systems)
 PERLBIN = perl
 
+prefix  = ${PREFIX}
 ## where you want things installed
-BINDIR  = $(HOME)/bin
-LIBDIR  = $(HOME)/lib/tRNAscan-SE
-MANDIR  = $(HOME)/man
+BINDIR  = $(prefix)/bin
+LIBDIR  = $(prefix)/share/tRNAscan-SE
+MANDIR  = $(prefix)/man
 
 ## NOTE !!  If you later manually move the location of 
 ## binaries or data files in the BINDIR or LIBDIR directories,
@@ -106,7 +107,7 @@
 
 MPOBJ = mpviterbi.o mp-dbviterbi.o
 
-all: 	$(PROGS) tRNAscanSE setpaths
+all: 	$(PROGS) tRNAscanSE
 
 covels-SE:  $(OBJ) scan_main.o
 	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
@@ -178,7 +179,7 @@
 	@echo ""
 	@rm -f testrun.out
 	@echo "tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa"
-	@if tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \
+	@if ./tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \
 	then echo ""; \
 	else echo "tRNAscan-SE did NOT complete properly."; fi
 	@if diff testrun.out testrun.ref; \