--- a/Makefile
+++ b/Makefile
@@ -20,9 +20,9 @@
 PERLBIN = perl
 
 ## where you want things installed
-BINDIR  = $(HOME)/bin
-LIBDIR  = $(HOME)/lib/tRNAscan-SE
-MANDIR  = $(HOME)/man
+BINDIR = $(EPREFIX)/usr/bin
+LIBDIR = $(EPREFIX)/usr/share/trnascan-se
+MANDIR = $(EPREFIX)/usr/share/man
 
 ## NOTE !!  If you later manually move the location of 
 ## binaries or data files in the BINDIR or LIBDIR directories,
@@ -33,10 +33,8 @@
 TEMPDIR = /tmp
 
 ## your compiler
-CC = gcc	  # GNU cc (if available) otherwise use vendor's cc
 
 ## any special compiler flags you want
-CFLAGS = -O    # ok for most machines (remove -O for DEC OSF/1 cc compiler)
 
 ## machine specific definitions
 #  You shouldn't need any. The specific #define's in squid are historical.
@@ -58,7 +56,7 @@
 #######
 
 SHELL  = /bin/sh
-LIBS   = -lm
+LIBS   += -lm
 .SUFFIXES : .c .o
 
 DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history
@@ -109,20 +107,20 @@
 all: 	$(PROGS) tRNAscan-SE setpaths
 
 covels-SE:  $(OBJ) scan_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
 
 coves-SE: $(OBJ) score_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
 
 eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
+	$(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \
 	pavesi.o $(SQUIDOBJ) $(LIBS)
 
-trnascan-1.4: trnascan.o
-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
+trnascan-1.4: trnascan.c
+	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
 
 tRNAscan-SE:
-	$(PERLDIR)/$(PERLBIN) checkversion.pl
+	$(PERLBIN) checkversion.pl
 	sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \
 	sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \
 	sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \
@@ -200,11 +198,11 @@
 noambig: trnascan-1.4-NA eufindtRNA-NA
 
 trnascan-1.4-NA:  trnascan.o
-	$(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c
+	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c
 
 eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o
-	$(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 
-	$(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \
+	$(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 
+	$(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \
 	pavesi-NA.o $(SQUIDOBJ) $(LIBS)	
 
 
@@ -220,7 +218,7 @@
 	rmdir -ps $(MANDIR)
 
 .c.o:
-	$(CC) $(CFLAGS) $(MDEFS) -c $<		
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<		
 
 ## programs from Sean Eddy's sequence i/o function library not
 ## needed for tRNAscan-SE but included for their utility
@@ -233,16 +231,16 @@
 	cp $(UTILS) $(BINDIR)/.
 
 reformat: $(SQUIDOBJ) reformat_main.o
-	$(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)
 
 revcomp: $(SQUIDOBJ) revcomp_main.o
-	$(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)
 
 seqstat: $(SQUIDOBJ) seqstat_main.o
-	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)
 
 shuffle: $(SQUIDOBJ) shuffle_main.o
-	$(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)
 
 ## other programs in Cove package (below) not needed for
 ## tRNAscan-SE, but are included for users who wish to apply
@@ -255,25 +253,25 @@
 	cp $(COVE_SUITE) $(BINDIR)/.
 
 covea: $(OBJ) align_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)
 
 coveb: $(OBJ) build_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)
 
 covee: $(OBJ) emit_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)
 
 covet: $(OBJ) train_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)
 
 covels:  $(OBJ) scan_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)
 
 coves: $(OBJ) score_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)
 
 structcheck: $(OBJ) structcheck_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)
 
 
 ## Maspar memory limits