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###################################################
#
# Makefile for mothur
#
###################################################
#
# Macros
#
# 64BIT_VERSION - set to no if you are using a 32bit arch.
# OPTIMIZE - yes will increase speed of executable.
# USEREADLINE - link with readline libraries. Must have readline installed. Windows set to no.
# USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files.
# BOOST_LIBRARY_DIR - location of boost libraries
# BOOST_INCLUDE_DIR - location of boost include files
# MOTHUR_FILES - default location for mothur to look for input files at runtime. Most often used for reference files.
64BIT_VERSION ?= yes
USEREADLINE ?= no
USEBOOST ?= no
RELEASE_DATE = "\"09/01/2017\""
VERSION = "\"1.40.0\""
# Optimize to level 3:
CXXFLAGS += -O3
#CPP_11
CXXFLAGS += -std=c++11
ifeq ($(strip $(64BIT_VERSION)),yes)
#if you using cygwin to build Windows the following line
CXX = x86_64-w64-mingw32-g++
CC = x86_64-w64-mingw32-g++
TARGET_ARCH += -m64 -static
CXXFLAGS += -DBIT_VERSION
endif
CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
# INCLUDE directories for mothur
VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/metastats:source/randomforest:source/read:source/svm
skipUchime := source/uchime_src/
subdirs := $(sort $(dir $(filter-out $(skipUchime), $(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) uchime
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
strip mothur
uchime:
cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
install : 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)
@rm -f uchime
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