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updated Makefiles to write to macosx and linux in bin
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ravel-lab committed Sep 6, 2024
1 parent 4d729a5 commit d96b03a
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Showing 34 changed files with 2,183 additions and 17 deletions.
2 changes: 1 addition & 1 deletion src/linux/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ MKDIR = mkdir -p
create-build-dir := $(shell $(CHK_DIR_EXISTS) .build || $(MKDIR) .build)

SRCDIR = .
BINDIR = ../bin
BINDIR = ../../bin/linux
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))
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138 changes: 138 additions & 0 deletions src/linux/Makefile.bu
Original file line number Diff line number Diff line change
@@ -0,0 +1,138 @@

#############################################################################
# Makefile for building classify
#############################################################################

# Copyright (C) 2016 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 = 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

####### Files

create-build-dir := $(shell $(CHK_DIR_EXISTS) .build || $(MKDIR) .build)

SRCDIR = .
BINDIR = ../bin
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))

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 \

####### Build rules

classify: $(OBJECTS)
$(CXX) $(FLAGS) $(OBJECTS) -o $(BINDIR)/classify

$(BUILDDIR)/classify.o: $(SRCDIR)/classify.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/classify.o $(SRCDIR)/classify.cc

$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc

$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c

$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc

$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc

$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c

$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc

$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc

$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c

$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc

$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc


$(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



clean:
-$(DEL_FILE) $(OBJECTS)
-$(DEL_FILE) *~ core *.core




distclean: clean
-$(DEL_FILE) $(TARGET)
-$(DEL_FILE) Makefile
2 changes: 1 addition & 1 deletion src/macosx/Makefile_buildMC
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ MKDIR = mkdir -p
####### Files

SRCDIR = .
BINDIR = ../bin
BINDIR = ../../bin/macosx
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))
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138 changes: 138 additions & 0 deletions src/macosx/Makefile_buildMC.bu
Original file line number Diff line number Diff line change
@@ -0,0 +1,138 @@

#############################################################################
# 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

####### Files

SRCDIR = .
BINDIR = ../bin
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))
create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR))

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 \

####### Build rules

buildMC: $(OBJECTS)
$(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/buildMC

$(BUILDDIR)/buildMC.o: $(SRCDIR)/buildMC.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/buildMC.o $(SRCDIR)/buildMC.cc

$(BUILDDIR)/IOCppUtilities.o: $(SRCDIR)/IOCppUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o $(SRCDIR)/IOCppUtilities.cc

$(BUILDDIR)/IOCUtilities.o: $(SRCDIR)/IOCUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o $(SRCDIR)/IOCUtilities.c

$(BUILDDIR)/DNAsequence.o: $(SRCDIR)/DNAsequence.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/DNAsequence.o $(SRCDIR)/DNAsequence.cc

$(BUILDDIR)/StatUtilities.o: $(SRCDIR)/StatUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/StatUtilities.o $(SRCDIR)/StatUtilities.cc

$(BUILDDIR)/CUtilities.o: $(SRCDIR)/CUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o $(SRCDIR)/CUtilities.c

$(BUILDDIR)/CppUtilities.o: $(SRCDIR)/CppUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o $(SRCDIR)/CppUtilities.cc

$(BUILDDIR)/strings.o: $(SRCDIR)/strings.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o $(SRCDIR)/strings.cc

$(BUILDDIR)/CStatUtilities.o: $(SRCDIR)/CStatUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CStatUtilities.o $(SRCDIR)/CStatUtilities.c

$(BUILDDIR)/CppStatUtilities.o: $(SRCDIR)/CppStatUtilities.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppStatUtilities.o $(SRCDIR)/CppStatUtilities.cc

$(BUILDDIR)/Newick.o: $(SRCDIR)/Newick.hh $(SRCDIR)/Newick.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o $(SRCDIR)/Newick.cc


$(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



clean:
-$(DEL_FILE) $(OBJECTS)
-$(DEL_FILE) *~ core *.core




distclean: clean
-$(DEL_FILE) $(TARGET)
-$(DEL_FILE) Makefile
2 changes: 1 addition & 1 deletion src/macosx/Makefile_buildModelTree
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ MKDIR = mkdir -p
####### Files

SRCDIR = .
BINDIR = ../bin
BINDIR = ../../bin/macosx
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))
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76 changes: 76 additions & 0 deletions src/macosx/Makefile_buildModelTree.bu
Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@

####### 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 = -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

####### Files

SRCDIR = .
BINDIR = ../bin
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))
create-bin-dir := $(shell $(CHK_DIR_EXISTS) $(BINDIR) || $(MKDIR) $(BINDIR))

OBJECTS = $(BUILDDIR)/buildModelTree.o \
$(BUILDDIR)/Newick.o \
$(BUILDDIR)/IOCUtilities.o \
$(BUILDDIR)/IOCppUtilities.o \
$(BUILDDIR)/CppUtilities.o \
$(BUILDDIR)/CUtilities.o \
$(BUILDDIR)/strings.o

buildModelTree: $(OBJECTS)
$(LINK) $(OBJECTS) $(LDFLAGS) -o $(BINDIR)/buildModelTree

$(BUILDDIR)/buildModelTree.o: buildModelTree.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -I$(SRCDIR) -o $(BUILDDIR)/buildModelTree.o buildModelTree.cc

$(BUILDDIR)/Newick.o: Newick.hh Newick.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/Newick.o Newick.cc

$(BUILDDIR)/IOCUtilities.o: IOCUtilities.h IOCUtilities.c
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCUtilities.o IOCUtilities.c

$(BUILDDIR)/IOCppUtilities.o: IOCppUtilities.cc IOCppUtilities.hh
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/IOCppUtilities.o IOCppUtilities.cc

$(BUILDDIR)/CppUtilities.o: CppUtilities.cc CppUtilities.hh
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/CppUtilities.o CppUtilities.cc

$(BUILDDIR)/CUtilities.o: CUtilities.c CUtilities.h
$(CC) -c $(CFLAGS) $(INCPATH) -o $(BUILDDIR)/CUtilities.o CUtilities.c

$(BUILDDIR)/strings.o: strings.cc
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o $(BUILDDIR)/strings.o strings.cc

clean:
rm -f $(BUILDDIR)/*.o

clean-all:
rm -rf $(BUILDDIR) $(BINDIR)/readNewick
2 changes: 1 addition & 1 deletion src/macosx/Makefile_clError
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ MKDIR = mkdir -p
####### Files

SRCDIR = .
BINDIR = ../bin
BINDIR = ../../bin/macosx
BUILDDIR= .build

create-build-dir := $(shell $(CHK_DIR_EXISTS) $(BUILDDIR) || $(MKDIR) $(BUILDDIR))
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