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updated Makefiles to write to macosx and linux in bin
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############################################################################# | ||
# Makefile for building classify | ||
############################################################################# | ||
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# Copyright (C) 2016 Pawel Gajer [email protected] and Jacques Ravel [email protected] | ||
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# Permission to use, copy, modify, and distribute this software and its | ||
# documentation with or without modifications and for any purpose and | ||
# without fee is hereby granted, provided that any copyright notices | ||
# appear in all copies and that both those copyright notices and this | ||
# permission notice appear in supporting documentation, and that the | ||
# names of the contributors or copyright holders not be used in | ||
# advertising or publicity pertaining to distribution of the software | ||
# without specific prior permission. | ||
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||
# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | ||
# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | ||
# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | ||
# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | ||
# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | ||
# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | ||
# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | ||
# OR PERFORMANCE OF THIS SOFTWARE. | ||
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####### Compiler, tools and options | ||
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CC = gcc #gcc-4.0 | ||
CXX = g++ #g++-4.0 | ||
FLAGS = -g # -fopenmp # -O2 # -g -O2 | ||
CFLAGS = $(FLAGS) -Wall -D__SIM_SSE3 -O2 -D_GNU_SOURCE -dynamic -msse3 -fomit-frame-pointer -funroll-loops # -D_USE_PTHREADS | ||
CXXFLAGS = $(FLAGS) -Wall -D__SIM_SSE3 -O2 -D_GNU_SOURCE -dynamic -msse3 -fomit-frame-pointer -funroll-loops # -D_USE_PTHREADS | ||
INCPATH = -Isrc | ||
LINK = g++ | ||
LIBS = -lm # -L../../lib -lkmerstats | ||
AR = ar cq | ||
RANLIB = ranlib -s | ||
TAR = tar -cf | ||
COMPRESS = gzip -9f | ||
COPY = cp -f | ||
SED = sed | ||
COPY_FILE = cp -f | ||
COPY_DIR = cp -f -R | ||
INSTALL_FILE = $(COPY_FILE) | ||
INSTALL_DIR = $(COPY_DIR) | ||
INSTALL_PROGRAM = $(COPY_FILE) | ||
DEL_FILE = rm -f | ||
SYMLINK = ln -sf | ||
DEL_DIR = rmdir | ||
MOVE = mv -f | ||
CHK_DIR_EXISTS= test -d | ||
MKDIR = mkdir -p | ||
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####### Files | ||
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create-build-dir := $(shell $(CHK_DIR_EXISTS) .build || $(MKDIR) .build) | ||
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SRCDIR = . | ||
BINDIR = ../bin | ||
BUILDDIR= .build | ||
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create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) | ||
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OBJECTS = $(BUILDDIR)/classify.o \ | ||
$(BUILDDIR)/IOCUtilities.o \ | ||
$(BUILDDIR)/IOCppUtilities.o \ | ||
$(BUILDDIR)/MarkovChains2.o \ | ||
$(BUILDDIR)/CUtilities.o \ | ||
$(BUILDDIR)/CppUtilities.o \ | ||
$(BUILDDIR)/strings.o \ | ||
$(BUILDDIR)/CStatUtilities.o \ | ||
$(BUILDDIR)/CppStatUtilities.o \ | ||
$(BUILDDIR)/StatUtilities.o \ | ||
$(BUILDDIR)/DNAsequence.o \ | ||
$(BUILDDIR)/Newick.o \ | ||
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####### Build rules | ||
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classify: $(OBJECTS) | ||
$(CXX) $(FLAGS) $(OBJECTS) -o $(BINDIR)/classify | ||
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$(BUILDDIR)/classify.o: $(SRCDIR)/classify.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/classify.o $(SRCDIR)/classify.cc | ||
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$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc | ||
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$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c | ||
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$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc | ||
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$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc | ||
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$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c | ||
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$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc | ||
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$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc | ||
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$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c | ||
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$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc | ||
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$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc | ||
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$(BUILDDIR)/MarkovChains2.o: $(SRCDIR)/MarkovChains2.cc $(SRCDIR)/MarkovChains2.hh \ | ||
$(SRCDIR)/CUtilities.h \ | ||
$(SRCDIR)/CUtilities.c \ | ||
$(SRCDIR)/CppUtilities.hh \ | ||
$(SRCDIR)/CppUtilities.cc \ | ||
$(SRCDIR)/strings.hh \ | ||
$(SRCDIR)/strings.cc \ | ||
$(SRCDIR)/DNAsequence.hh \ | ||
$(SRCDIR)/DNAsequence.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains2.o $(SRCDIR)/MarkovChains2.cc | ||
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clean: | ||
-$(DEL_FILE) $(OBJECTS) | ||
-$(DEL_FILE) *~ core *.core | ||
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distclean: clean | ||
-$(DEL_FILE) $(TARGET) | ||
-$(DEL_FILE) Makefile |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,138 @@ | ||
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############################################################################# | ||
# Makefile for building classify | ||
############################################################################# | ||
|
||
# Copyright (C) 2017 Pawel Gajer [email protected] and Jacques Ravel [email protected] | ||
|
||
# Permission to use, copy, modify, and distribute this software and its | ||
# documentation with or without modifications and for any purpose and | ||
# without fee is hereby granted, provided that any copyright notices | ||
# appear in all copies and that both those copyright notices and this | ||
# permission notice appear in supporting documentation, and that the | ||
# names of the contributors or copyright holders not be used in | ||
# advertising or publicity pertaining to distribution of the software | ||
# without specific prior permission. | ||
|
||
# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | ||
# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | ||
# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | ||
# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | ||
# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | ||
# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | ||
# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | ||
# OR PERFORMANCE OF THIS SOFTWARE. | ||
|
||
####### Compiler, tools and options | ||
|
||
CC = clang #gcc #gcc-4.0 | ||
CXX = clang #g++ #g++-4.0 | ||
LINK = clang #g++ | ||
LDFLAGS = -std=c++11 -lc++abi -lstdc++ | ||
FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter | ||
CFLAGS = $(FLAGS) | ||
CXXFLAGS = $(FLAGS) | ||
INCPATH = -Isrc | ||
LIBS = -lm # -L../../lib -lkmerstats | ||
AR = ar cq | ||
RANLIB = ranlib -s | ||
TAR = tar -cf | ||
COMPRESS = gzip -9f | ||
COPY = cp -f | ||
SED = sed | ||
COPY_FILE = cp -f | ||
COPY_DIR = cp -f -R | ||
INSTALL_FILE = $(COPY_FILE) | ||
INSTALL_DIR = $(COPY_DIR) | ||
INSTALL_PROGRAM = $(COPY_FILE) | ||
DEL_FILE = rm -f | ||
SYMLINK = ln -sf | ||
DEL_DIR = rmdir | ||
MOVE = mv -f | ||
CHK_DIR_EXISTS= test -d | ||
MKDIR = mkdir -p | ||
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####### Files | ||
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SRCDIR = . | ||
BINDIR = ../bin | ||
BUILDDIR= .build | ||
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create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) | ||
create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) | ||
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OBJECTS = $(BUILDDIR)/buildMC.o \ | ||
$(BUILDDIR)/IOCUtilities.o \ | ||
$(BUILDDIR)/IOCppUtilities.o \ | ||
$(BUILDDIR)/MarkovChains.o \ | ||
$(BUILDDIR)/CUtilities.o \ | ||
$(BUILDDIR)/CppUtilities.o \ | ||
$(BUILDDIR)/strings.o \ | ||
$(BUILDDIR)/CStatUtilities.o \ | ||
$(BUILDDIR)/CppStatUtilities.o \ | ||
$(BUILDDIR)/StatUtilities.o \ | ||
$(BUILDDIR)/DNAsequence.o \ | ||
$(BUILDDIR)/Newick.o \ | ||
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####### Build rules | ||
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buildMC: $(OBJECTS) | ||
$(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/buildMC | ||
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$(BUILDDIR)/buildMC.o: $(SRCDIR)/buildMC.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/buildMC.o $(SRCDIR)/buildMC.cc | ||
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$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc | ||
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$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c | ||
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$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc | ||
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$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc | ||
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$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c | ||
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$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc | ||
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$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc | ||
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$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c | ||
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$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc | ||
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$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc | ||
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$(BUILDDIR)/MarkovChains.o: $(SRCDIR)/MarkovChains.cc $(SRCDIR)/MarkovChains.hh \ | ||
$(SRCDIR)/CUtilities.h \ | ||
$(SRCDIR)/CUtilities.c \ | ||
$(SRCDIR)/CppUtilities.hh \ | ||
$(SRCDIR)/CppUtilities.cc \ | ||
$(SRCDIR)/strings.hh \ | ||
$(SRCDIR)/strings.cc \ | ||
$(SRCDIR)/DNAsequence.hh \ | ||
$(SRCDIR)/DNAsequence.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/MarkovChains.o $(SRCDIR)/MarkovChains.cc | ||
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clean: | ||
-$(DEL_FILE) $(OBJECTS) | ||
-$(DEL_FILE) *~ core *.core | ||
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distclean: clean | ||
-$(DEL_FILE) $(TARGET) | ||
-$(DEL_FILE) Makefile |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,76 @@ | ||
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####### Compiler, tools and options | ||
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||
CC = clang #gcc #gcc-4.0 | ||
CXX = clang #g++ #g++-4.0 | ||
LINK = clang #g++ | ||
LDFLAGS = -std=c++11 -lc++abi -lstdc++ | ||
FLAGS = -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type # -D_USE_PTHREADS # -fopenmp # -O2 # -g -O2 -Wunused-parameter | ||
CFLAGS = $(FLAGS) | ||
CXXFLAGS = $(FLAGS) | ||
INCPATH = -I../src | ||
LIBS = # -lm # -L../../lib -lkmerstats | ||
AR = ar cq | ||
RANLIB = ranlib -s | ||
TAR = tar -cf | ||
COMPRESS = gzip -9f | ||
COPY = cp -f | ||
SED = sed | ||
COPY_FILE = cp -f | ||
COPY_DIR = cp -f -R | ||
INSTALL_FILE = $(COPY_FILE) | ||
INSTALL_DIR = $(COPY_DIR) | ||
INSTALL_PROGRAM = $(COPY_FILE) | ||
DEL_FILE = rm -f | ||
SYMLINK = ln -sf | ||
DEL_DIR = rmdir | ||
MOVE = mv -f | ||
CHK_DIR_EXISTS= test -d | ||
MKDIR = mkdir -p | ||
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####### Files | ||
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SRCDIR = . | ||
BINDIR = ../bin | ||
BUILDDIR= .build | ||
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create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR)) | ||
create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR)) | ||
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OBJECTS = $(BUILDDIR)/buildModelTree.o \ | ||
$(BUILDDIR)/Newick.o \ | ||
$(BUILDDIR)/IOCUtilities.o \ | ||
$(BUILDDIR)/IOCppUtilities.o \ | ||
$(BUILDDIR)/CppUtilities.o \ | ||
$(BUILDDIR)/CUtilities.o \ | ||
$(BUILDDIR)/strings.o | ||
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buildModelTree: $(OBJECTS) | ||
$(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/buildModelTree | ||
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$(BUILDDIR)/buildModelTree.o: buildModelTree.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -I$(SRCDIR) -o $(BUILDDIR)/buildModelTree.o buildModelTree.cc | ||
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$(BUILDDIR)/Newick.o: Newick.hh Newick.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o Newick.cc | ||
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$(BUILDDIR)/IOCUtilities.o: IOCUtilities.h IOCUtilities.c | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o IOCUtilities.c | ||
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$(BUILDDIR)/IOCppUtilities.o: IOCppUtilities.cc IOCppUtilities.hh | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o IOCppUtilities.cc | ||
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$(BUILDDIR)/CppUtilities.o: CppUtilities.cc CppUtilities.hh | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o CppUtilities.cc | ||
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$(BUILDDIR)/CUtilities.o: CUtilities.c CUtilities.h | ||
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o CUtilities.c | ||
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$(BUILDDIR)/strings.o: strings.cc | ||
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o strings.cc | ||
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clean: | ||
rm -f $(BUILDDIR)/*.o | ||
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clean-all: | ||
rm -rf $(BUILDDIR) $(BINDIR)/readNewick |
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