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--- makefile.orig 2019-08-29 18:03:23 UTC
+++ makefile
@@ -7,23 +7,32 @@
#
# Constants
-CXX=g++
+# Default to g++ if not set by make args or environment
+CXX?=g++
#-O0 -g will turn on debugging
#The rule of thumb:
#When you need to debug, use -O0 (and -g to generate debugging symbols.)
#When you are preparing to ship it, use -O2.
#When you use gentoo, use -O3...!
#When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.)
-CXX_FLAGS=-Wall -g -stdlib=libstdc++
+# Use canonincal compiler variables, which may be provided by build env
+CXXFLAGS?=-Wall -g -stdlib=libstdc++
SRC=src
CONF=conf
HMM_SRC=$(SRC)/hmm
UTIL_SRC=$(SRC)/util
-BOOST=/usr/local/boost_1_52_0
+BOOST?=/usr/local/boost_1_52_0
INCLUDES=-I./$(SRC) -I./$(HMM_SRC) -I./$(UTIL_SRC) -isystem$(BOOST)
-LIBRARY_PATHS=-Llib/macosx
+LIBRARY_PATHS?=-Llib/macosx
LIBRARIES=-lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread
+# Installation target with destdir support
+DESTDIR?=.
+PREFIX?=/usr/local
+MKDIR?=mkdir
+INSTALL?=install
+STRIP?= # empty, set to -s to install stripped binary
+
# Generated directories which are generated in this script and cleaned up with 'make clean'
BUILD=build
OBJ=$(BUILD)/obj
@@ -35,18 +44,21 @@ directories:
# Create object files into the OBJ directory from cpp files in the SRC directory.
$(OBJ)/%.o: $(SRC)/%.cpp directories
- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
$(OBJ)/%.o: $(HMM_SRC)/%.cpp directories
- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
$(OBJ)/%.o: $(UTIL_SRC)/%.cpp directories
- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
-all: clean haplohseq
+all: haplohseq test
haplohseq: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o
- $(CXX) -o $(BIN)/$@ $(CXX_FLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES)
- cp -r $(CONF) $(BIN)/.
-
+ $(CXX) -o $(BIN)/$@ $(CXXFLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+install:
+ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
+ $(INSTALL) -c $(STRIP) $(BIN)/* $(DESTDIR)$(PREFIX)/bin
+
clean:
rm -rf $(BUILD)
@@ -74,28 +86,28 @@ test: FreqPhaseTest HaplohSeqTest HmmTest InputProcess
# Create test object files into the OBJ directory from cpp files in the SRC directory.
$(TEST_BIN)/%.o: $(TEST_SRC)/%.cpp directories test_directory
- $(CXX) $(CXX_FLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $<
+ $(CXX) $(CXXFLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $<
HaplohSeqTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
FreqPhaseTest: $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
HmmTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
InputProcessorTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
MathUtilTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
ReporterTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
ThreadPoolTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o
- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES)
+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
############################## END TEST LOGIC ##############################
|
