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|
--- 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
|
