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#compress for release command
#zip -r {filename.zip} {foldername}
USEREADLINE ?= yes
USEBOOST ?= yes
USEHDF5 ?= yes
USEGSL ?= yes
LOGFILE_NAME ?= yes
VERSION = "\"1.47.0\""
RELEASE_DATE = "\"1/21/22\""
# Optimize to level 3:
CXXFLAGS += -O3 -std=c++11
LDFLAGS += -std=c++11 -pthreads
ifeq ($(strip $(LOGFILE_NAME)),yes)
LOGFILE_NAME="\"mothur.logfile\""
endif
#if you are a mac user use the following line
#TARGET_ARCH += -arch x86_64
#if you using cygwin to build Windows the following line
#CXX = x86_64-w64-mingw32-g++
#CC = x86_64-w64-mingw32-g++
#TARGET_ARCH += -m64 -static
#if you are a linux user use the following line
#CXXFLAGS += -mtune=generic
CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
# if you do not want to use the readline library, set this to no.
# make sure you have the library installed
ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
LIBS += -lreadline
endif
#The boost libraries allow you to read gz files.
ifeq ($(strip $(USEBOOST)),yes)
#statically link so the boost install is not required on users machine
BOOST_INCLUDE_DIR="/usr/local/include"
BOOST_LIBRARY_DIR="/usr/local/lib"
#windows paths
#BOOST_INCLUDE_DIR="/usr/x86_64-w64-mingw32/sys-root/mingw/include"
#BOOST_LIBRARY_DIR="/usr/x86_64-w64-mingw32/sys-root/mingw/lib"
CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
LIBS += ${BOOST_LIBRARY_DIR}/libboost_system.a
LIBS += ${BOOST_LIBRARY_DIR}/libboost_iostreams.a
LIBS += ${BOOST_LIBRARY_DIR}/libboost_filesystem.a
LIBS += ${BOOST_LIBRARY_DIR}/libz.a
endif
#User specified HDF5 library
ifeq ($(strip $(USEHDF5)),yes)
HDF5_INCLUDE_DIR="/usr/local/include"
HDF5_LIBRARY_DIR="/usr/local/lib"
LDFLAGS += -L ${HDF5_LIBRARY_DIR}
LIBS += ${HDF5_LIBRARY_DIR}/libhdf5_hl_cpp.a
LIBS += ${HDF5_LIBRARY_DIR}/libhdf5_cpp.a
LIBS += ${HDF5_LIBRARY_DIR}/libhdf5_hl.a
LIBS += ${HDF5_LIBRARY_DIR}/libhdf5.a
CXXFLAGS += -DUSE_HDF5 -I ${HDF5_INCLUDE_DIR}
endif
#User specified GSL library
ifeq ($(strip $(USEGSL)),yes)
GSL_LIBRARY_DIR ?= "\"/usr/local/gsl/lib\""
GSL_INCLUDE_DIR ?= "\"/usr/local/gsl/include\""
#windows paths
#GSL_INCLUDE_DIR="/usr/x86_64-w64-mingw32/sys-root/mingw/include"
#GSL_LIBRARY_DIR="/usr/x86_64-w64-mingw32/sys-root/mingw/lib"
LDFLAGS += -L ${GSL_LIBRARY_DIR}
LIBS += ${GSL_LIBRARY_DIR}/libgsl.a
LIBS += ${GSL_LIBRARY_DIR}/libgslcblas.a
CXXFLAGS += -DUSE_GSL -I ${GSL_INCLUDE_DIR}
endif
#
# INCLUDE directories for mothur
#
#
VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
skipUchime := source/uchime_src/
subdirs := $(sort $(dir $(filter-out $(skipUchime), source/, $(wildcard source/*/))))
subDirIncludes = $(patsubst %, -I %, $(subdirs))
subDirLinking = $(patsubst %, -L%, $(subdirs))
CXXFLAGS += -I. $(subDirIncludes)
LDFLAGS += $(subDirLinking)
#
# Get the list of all .cpp files, rename to .o files
#
OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
mothur : $(OBJECTS)
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
strip mothur
%.o : %.c %.h
$(COMPILE.c) $(OUTPUT_OPTION) $<
%.o : %.cpp %.h
$(COMPILE.cpp) $(OUTPUT_OPTION) $<
%.o : %.cpp %.hpp
$(COMPILE.cpp) $(OUTPUT_OPTION) $<
clean :
@rm -f $(OBJECTS)
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