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Makefile_legacy
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Makefile_legacy
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#for libdivsufsort, cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="../../lib" .. -DBUILD_DIVSUFSORT64:BOOL=ON
#when calling, allow for setting the DESTDIR env variable
#when calling, allow for the #DONT_INSTALL_DIVSUFSORT env variable
#todo: documentation for calling git clone with --recurse-submodules or use git submodule init & git submodule update
SHELL = /bin/sh
PREFIX = /usr/local
AWFMINDEX_PROJECT_NAME = awfmindex
AWFMINDEX_MAJOR_VERSION_NUM = 2
AWFMINDEX_MINOR_VERSION_NUM = 0
AWFMINDEX_VERSION = $(MAJOR).$(MINOR)
#filenames
AWFMINDEX_HEADER_FILENAME = AwFmIndex.h
AWFMINDEX_SHARED_LIB_FILENAME = libawfmindex.so
AWFMINDEX_STATIC_LIB_FILENAME = libawfmindex.a
LIBDIVSUFSORT_HEADER_FILENAME = divsufsort64.h
LIBDIVSUFSORT_STATIC_LIB_FILENAME = libdivsufsort64.a
FASTA_VECTOR_HEADER_FILENAME = FastaVector.h
FASTA_VECTOR_STRING_HEADER_FILENAME = FastaVectorString.h
FASTA_VECTOR_METADATA_HEADER_FILENAME = FastaVectorMetadataVector.h
FASTA_VECTOR_STATIC_LIB_FILENAME = libfastavector.a
#determine the current operating system and architecture.
OS_NAME = $(shell uname -s)
ARCH_NAME = $(shell uname -p) #currently unused.
ifeq ($(OS_NAME), Darwin)
AWFMINDEX_SHARED_LIB_FILENAME = libawfmindex.dylib
endif
#directories
AWFMINDEX_PROJECT_DIR := $(shell dirname $(realpath $(firstword $(MAKEFILE_LIST))))
AWFMINDEX_BUILD_DIR = $(AWFMINDEX_PROJECT_DIR)/build
AWFMINDEX_SRC_DIR = $(AWFMINDEX_PROJECT_DIR)/src
AWFMINDEX_BUILD_INCLUDE_DIR = $(AWFMINDEX_BUILD_DIR)/include
AWFMINDEX_BUILD_LIBRARY_DIR = $(AWFMINDEX_BUILD_DIR)/lib
AWFMINDEX_INSTALL_INCLUDE_DIR = $(DESTDIR)$(PREFIX)/include
AWFMINDEX_INSTALL_LIBRARY_DIR = $(DESTDIR)$(PREFIX)/lib
LIBDIVSUFSORT_PROJECT_DIR = $(AWFMINDEX_PROJECT_DIR)/lib/libdivsufsort
LIBDIVSUFSORT_BUILD_DIR = $(LIBDIVSUFSORT_PROJECT_DIR)/build
LIBDIVSUFSORT_BUILD_INCLUDE_DIR = $(LIBDIVSUFSORT_BUILD_DIR)/include
LIBDIVSUFSORT_BUILD_LIBRARY_DIR = $(LIBDIVSUFSORT_BUILD_DIR)/lib
FASTA_VECTOR_PROJECT_DIR = $(AWFMINDEX_PROJECT_DIR)/lib/FastaVector
FASTA_VECTOR_SRC_DIR = $(FASTA_VECTOR_PROJECT_DIR)/src
FASTA_VECTOR_BUILD_DIR = $(FASTA_VECTOR_PROJECT_DIR)/build
FASTA_VECTOR_BUILD_INCLUDE_DIR = $(FASTA_VECTOR_BUILD_DIR)/include
FASTA_VECTOR_BUILD_LIB_DIR = $(FASTA_VECTOR_BUILD_DIR)/lib
#file locations
AWFMINDEX_SRC_HEADER_FILE = $(AWFMINDEX_SRC_DIR)/$(AWFMINDEX_HEADER_FILENAME)
AWFMINDEX_BUILD_HEADER_FILE = $(AWFMINDEX_BUILD_INCLUDE_DIR)/$(AWFMINDEX_HEADER_FILENAME)
AWFMINDEX_BUILD_SHARED_LIB_FILE = $(AWFMINDEX_BUILD_LIBRARY_DIR)/$(AWFMINDEX_SHARED_LIB_FILENAME)
AWFMINDEX_BUILD_STATIC_LIB_FILE = $(AWFMINDEX_BUILD_LIBRARY_DIR)/$(AWFMINDEX_STATIC_LIB_FILENAME)
AWFMINDEX_INSTALL_HEADER_FILE = $(AWFMINDEX_INSTALL_INCLUDE_DIR)/$(AWFMINDEX_HEADER_FILENAME)
AWFMINDEX_INSTALL_STATIC_LIB_FILE = $(AWFMINDEX_INSTALL_LIBRARY_DIR)/$(AWFMINDEX_STATIC_LIB_FILENAME)
AWFMINDEX_INSTALL_SHARED_LIB_FILE = $(AWFMINDEX_INSTALL_LIBRARY_DIR)/$(AWFMINDEX_SHARED_LIB_FILENAME)
LIBDIVSUFSORT_BUILD_HEADER_FILE = $(LIBDIVSUFSORT_BUILD_INCLUDE_DIR)/$(LIBDIVSUFSORT_HEADER_FILENAME)
LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE = $(LIBDIVSUFSORT_BUILD_LIBRARY_DIR)/$(LIBDIVSUFSORT_STATIC_LIB_FILENAME)
LIBDIVSUFSORT_INSTALL_HEADER_FILE = $(AWFMINDEX_INSTALL_INCLUDE_DIR)/$(LIBDIVSUFSORT_HEADER_FILENAME)
FASTA_VECTOR_BUILD_HEADER_FILE = $(FASTA_VECTOR_SRC_DIR)/$(FASTA_VECTOR_HEADER_FILENAME)
FASTA_VECTOR_BUILD_STRING_HEADER_FILE = $(FASTA_VECTOR_SRC_DIR)/$(FASTA_VECTOR_STRING_HEADER_FILENAME)
FASTA_VECTOR_BUILD_METADATA_HEADER_FILE = $(FASTA_VECTOR_SRC_DIR)/$(FASTA_VECTOR_METADATA_HEADER_FILENAME)
FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE = $(FASTA_VECTOR_BUILD_LIB_DIR)/$(FASTA_VECTOR_STATIC_LIB_FILENAME)
FASTA_VECTOR_INSTALL_HEADER_FILE = $(AWFMINDEX_INSTALL_INCLUDE_DIR)/$(FASTA_VECTOR_HEADER_FILENAME)
FASTA_VECTOR_INSTALL_STRING_HEADER_FILE = $(AWFMINDEX_INSTALL_INCLUDE_DIR)/$(FASTA_VECTOR_STRING_HEADER_FILENAME)
FASTA_VECTOR_INSTALL_METADATA_HEADER_FILE = $(AWFMINDEX_INSTALL_INCLUDE_DIR)/$(FASTA_VECTOR_METADATA_HEADER_FILENAME)
LIBDIVSUFSORT_BUILD_HEADER_FILE_STATIC_DEST = $(AWFMINDEX_BUILD_INCLUDE_DIR)/$(LIBDIVSUFSORT_HEADER_FILENAME)
FASTA_VECTOR_BUILD_HEADER_FILE_DEST = $(AWFMINDEX_BUILD_INCLUDE_DIR)/$(FASTA_VECTOR_HEADER_FILENAME)
FASTA_VECTOR_BUILD_STRING_HEADER_FILE_DEST = $(AWFMINDEX_BUILD_INCLUDE_DIR)/$(FASTA_VECTOR_STRING_HEADER_FILENAME)
FASTA_VECTOR_BUILD_STRING_METADATA_FILE_DEST = $(AWFMINDEX_BUILD_INCLUDE_DIR)/$(FASTA_VECTOR_METADATA_HEADER_FILENAME)
LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE_DEST = $(AWFMINDEX_BUILD_LIBRARY_DIR)/$(LIBDIVSUFSORT_STATIC_LIB_FILENAME)
FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE_DEST = $(AWFMINDEX_BUILD_LIBRARY_DIR)/$(FASTA_VECTOR_STATIC_LIB_FILENAME)
LIBDIVSUFSORT_BUILD_SHARED_LIBRARY_FILE_DEST = $(AWFMINDEX_BUILD_LIBRARY_DIR)/$()
#if on a Mac system, CC may need to be overwritten with a makefile argument to compile with
#an actual GCC compiler instead of the clang that ships native with mac.
ARCH = $(shell uname -m)
CC ?= gcc
ifeq ($(ARCH),x86_64)
CFLAGS = -std=gnu11 -fpic -O3 -mtune=native -march=native -Wall -Wextra -fopenmp -mavx2
else
CFLAGS = -std=gnu11 -fpic -O3 -mtune=native -march=native -Wall -Wextra -fopenmp
endif
LDFLAGS = -shared -L$(LIBDIVSUFSORT_BUILD_LIBRARY_DIR) -L$(FASTA_VECTOR_BUILD_LIB_DIR) -I$(LIBDIVSUFSORT_BUILD_INCLUDE_DIR) -ldivsufsort64 -lfastavector # linking flags
SOURCE_FILES := $(wildcard $(AWFMINDEX_SRC_DIR)/*.c)
OBJECT_FILES := $(patsubst $(AWFMINDEX_SRC_DIR)/%, $(AWFMINDEX_BUILD_DIR)/%, $(SOURCE_FILES:.c=.o))
#rules
.PHONY: all
all: $(LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE) $(FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE) $(AWFMINDEX_BUILD_LIBRARY_DIR) $(OBJECT_FILES) $(AWFMINDEX_BUILD_HEADER_FILE)
$(CC) -fpic -fopenmp -o $(AWFMINDEX_BUILD_SHARED_LIB_FILE) $(OBJECT_FILES) $(LDFLAGS)
cp $(LIBDIVSUFSORT_BUILD_HEADER_FILE) $(LIBDIVSUFSORT_BUILD_HEADER_FILE_STATIC_DEST)
cp $(FASTA_VECTOR_BUILD_HEADER_FILE) $(FASTA_VECTOR_BUILD_HEADER_FILE_DEST)
cp $(FASTA_VECTOR_BUILD_STRING_HEADER_FILE) $(FASTA_VECTOR_BUILD_STRING_HEADER_FILE_DEST)gy
cp $(FASTA_VECTOR_BUILD_METADATA_HEADER_FILE) $(FASTA_VECTOR_BUILD_STRING_METADATA_FILE_DEST)
.PHONY: install
install:
mkdir -p $(DESTDIR)$(PREFIX)/lib
mkdir -p $(DESTDIR)$(PREFIX)/include
cp $(LIBDIVSUFSORT_BUILD_HEADER_FILE) $(LIBDIVSUFSORT_INSTALL_HEADER_FILE)
cp $(AWFMINDEX_SRC_HEADER_FILE) $(AWFMINDEX_INSTALL_HEADER_FILE)
cp $(FASTA_VECTOR_BUILD_HEADER_FILE) $(FASTA_VECTOR_INSTALL_HEADER_FILE)
cp $(FASTA_VECTOR_BUILD_STRING_HEADER_FILE) $(FASTA_VECTOR_INSTALL_STRING_HEADER_FILE)
cp $(FASTA_VECTOR_BUILD_METADATA_HEADER_FILE) $(FASTA_VECTOR_INSTALL_METADATA_HEADER_FILE)
ifneq ("$(wildcard $(AWFMINDEX_BUILD_SHARED_LIB_FILE))","")
cp $(AWFMINDEX_BUILD_SHARED_LIB_FILE) $(AWFMINDEX_INSTALL_SHARED_LIB_FILE)
endif
ifneq ("$(wildcard $(AWFMINDEX_BUILD_STATIC_LIB_FILE))","")
cp $(AWFMINDEX_BUILD_STATIC_LIB_FILE) $(AWFMINDEX_INSTALL_STATIC_LIB_FILE)
endif
#make the static libs
.PHONY: static
static: $(LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE) $(FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE) $(AWFMINDEX_BUILD_LIBRARY_DIR) $(OBJECT_FILES) $(AWFMINDEX_BUILD_HEADER_FILE)
ar rcs $(AWFMINDEX_BUILD_STATIC_LIB_FILE) $(OBJECT_FILES)
#make the libdivsufsort static lib copy in the build directory
cp $(LIBDIVSUFSORT_BUILD_HEADER_FILE) $(LIBDIVSUFSORT_BUILD_HEADER_FILE_STATIC_DEST)
cp $(FASTA_VECTOR_BUILD_HEADER_FILE) $(FASTA_VECTOR_BUILD_HEADER_FILE_DEST)
cp $(FASTA_VECTOR_BUILD_STRING_HEADER_FILE) $(FASTA_VECTOR_BUILD_STRING_HEADER_FILE_DEST)
cp $(FASTA_VECTOR_BUILD_METADATA_HEADER_FILE) $(FASTA_VECTOR_BUILD_STRING_METADATA_FILE_DEST)
cp $(LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE) $(LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE_DEST)
cp $(FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE) $(FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE_DEST)
clean:
rm -rf $(AWFMINDEX_BUILD_DIR)
cd $(LIBDIVSUFSORT_BUILD_DIR) && make clean
.PHONY: uninstall
uninstall:
rm -f $(AWFMINDEX_INSTALL_SHARED_LIB_FILE)
rm -f $(AWFMINDEX_INSTALL_STATIC_LIB_FILE)
rm -f $(AWFMINDEX_INSTALL_HEADER_FILE)
rm -f $(LIBDIVSUFSORT_INSTALL_HEADER_FILE)
rm -f $(FASTA_VECTOR_INSTALL_HEADER_FILE)
rm -f $(FASTA_VECTOR_INSTALL_STRING_HEADER_FILE)
rm -f $(FASTA_VECTOR_INSTALL_METADATA_HEADER_FILE)
rm -f $(LIBDIVSUFSORT_BUILD_HEADER_FILE_STATIC_DEST)
rm -f $(FASTA_VECTOR_BUILD_HEADER_FILE_DEST)
rm -f $(FASTA_VECTOR_BUILD_STRING_HEADER_FILE_DEST)
rm -f $(FASTA_VECTOR_BUILD_STRING_METADATA_FILE_DEST)
rm -f $(LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE_DEST)
rm -f $(FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE_DEST)
cd $(LIBDIVSUFSORT_BUILD_DIR) && make uninstall
cd $(FASTA_VECTOR_PROJECT_DIR) && make uninstall
# builds libdivsufsort into a static library
$(LIBDIVSUFSORT_BUILD_STATIC_LIBRARY_FILE): $(LIBDIVSUFSORT_PROJECT_DIR)/.git $(LIBDIVSUFSORT_BUILD_DIR) $(LIBDIVSUFSORT_PROJECT_DIR) $(AWFMINDEX_BUILD_DIR)
cd $(LIBDIVSUFSORT_BUILD_DIR) && cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_BUILD_TYPE="Release" -DUSE_OPENMP="ON" -DBUILD_SHARED_LIBS="OFF" -DBUILD_DIVSUFSORT64:BOOL=ON -DCMAKE_INSTALL_PREFIX="$(AWFMINDEX_BUILD_DIR)" .. && make
$(FASTA_VECTOR_BUILD_STATIC_LIBRARY_FILE): $(FASTA_VECTOR_PROJECT_DIR)/.git
cd $(FASTA_VECTOR_PROJECT_DIR) && make -f Makefile_legacy static
#create the object files from each c file in the src directory
$(AWFMINDEX_BUILD_DIR)/%.o: $(AWFMINDEX_SRC_DIR)/%.c
$(CC) $(CFLAGS) -c $< -o $@ -I $(LIBDIVSUFSORT_BUILD_INCLUDE_DIR) -I $(FASTA_VECTOR_BUILD_INCLUDE_DIR)
#initialize the libdivsufsort project submodule if not already done
$(LIBDIVSUFSORT_PROJECT_DIR)/.git:
git submodule init
git submodule update
$(FASTA_VECTOR_PROJECT_DIR)/.git:
git submodule init
git submodule update
#copy the AwFmIndex.h header to the build directory
$(AWFMINDEX_BUILD_HEADER_FILE): $(AWFMINDEX_BUILD_INCLUDE_DIR)
cp $(AWFMINDEX_SRC_HEADER_FILE) $(AWFMINDEX_BUILD_HEADER_FILE)
#make the libdivsufsort build directory if not already done
$(LIBDIVSUFSORT_BUILD_DIR): $(LIBDIVSUFSORT_PROJECT_DIR)/.git
mkdir -p $(LIBDIVSUFSORT_BUILD_DIR)
#make the AwFmIndex build lib directory
$(AWFMINDEX_BUILD_LIBRARY_DIR):
mkdir -p $(AWFMINDEX_BUILD_LIBRARY_DIR)
#make the AwFmIndex build lib directory
$(AWFMINDEX_BUILD_DIR):
mkdir -p $(AWFMINDEX_BUILD_DIR)
#make the AwFmIndex build include directory
$(AWFMINDEX_BUILD_INCLUDE_DIR):
mkdir -p $(AWFMINDEX_BUILD_INCLUDE_DIR)