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Author: Steffen Moeller
Last-Update: 2018-05-04 18:33:03 +0200
Description: Adapt Makefile to accept Debian preset compiler options
Index: soapaligner/Makefile
===================================================================
--- soapaligner.orig/Makefile
+++ soapaligner/Makefile
@@ -1,33 +1,40 @@
-SHELL = /bin/sh
-PROG = soap
-DEBUG = NO
-PROFILE = NO
-PTHREADS = YES
-CC = gcc
-DEBUG_FLAGS = -g3 -Wall -O2
-PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg
-RELEASE_FLAGS = -msse3 -O3 -static -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
-STATIC_FLAGS = -static
-DFLAGS = -DMAKE_TIME=\""`date`"\"
-LIBS = -lm
+SHELL ?= /bin/sh
+PROG ?= soap
+DEBUG ?= NO
+STATIC ?= NO
+PROFILE ?= NO
+PTHREADS ?= YES
+CC ?= gcc
+DEBUG_FLAGS ?= -g3 -Wall -O2
+PROFILE_FLAGS ?= -fprofile-arcs -ftest-coverage -pg
+RELEASE_FLAGS ?= -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
+STATIC_FLAGS ?= -static
+DFLAGS ?= -DMAKE_TIME=\""`date`"\"
+LDFLAGS ?=
+LIBS ?= -lm
#TARBALL_EXCLUDE = "*.(o,gz,zip)"
#ZIP_EXCLUDE = *.o *.gz *.zip
+ifeq (YES, $(STATIC))
+ CFLAGS += $(STATIC_FLAGS)
+endif
+
ifeq (YES, $(DEBUG))
- CFLAGS = $(DEBUG_FLAGS) $(STATIC_FLAGS)
- DFLAGS += -DDEBUG
+ CFLAGS += $(DEBUG_FLAGS) $(STATIC_FLAGS)
+ CFLAGS += -DDEBUG
# PTHREADS = NO
else
- CFLAGS = $(RELEASE_FLAGS) $(STATIC_FLAGS)
+ CFLAGS += $(RELEASE_FLAGS)
endif
ifeq (YES, $(PTHREADS))
LIBS += -lpthread
- DFLAGS += -DPTHREADS
+ CFLAGS += -DPTHREADS
endif
+CFLAGS += $(DFLAGS)
ifeq (YES, $(PROFILE))
- DFLAGS += $(PROFILE_FLAGS)
+ CFLAGS += $(PROFILE_FLAGS)
endif
OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o
@@ -35,12 +42,12 @@ OBJ = SeqIO.o MiscUtilities.o MemManager
.SUFFIX: .c .o
.c.o:
- $(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@
+ $(CC) -c $(CFLAGS) $< -o $@
all: $(PROG)
-$(PROG): $(OBJ) soap.o
- $(CC) $(CFLAGS) $(DFLAGS) $(OBJ) soap.o -o $@ $(LIBS)
+$(PROG): $(OBJ)
+ $(CC) $(CFLAGS) $(OBJ) -o $@ $(LDFLAGS) $(LIBS)
SeqIO.o:SeqIO.h
r250.o: r250.h
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