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|
#
# Sub directories containing source code, except for the main programs
SUBDIRS := src src/hmm src/thirdparty src/thirdparty/scrappie src/common src/alignment src/pore_model src/io src/basemods
#
# Set libraries, paths, flags and options
#
#Basic flags every build needs
LIBS = -lz
CXXFLAGS ?= -g -O3
CXXFLAGS += -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64
CFLAGS ?= -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64
LDFLAGS ?=
CXX ?= g++
CC ?= gcc
ifeq ($(zstd),1)
LDFLAGS += -lzstd
endif
# Change the value of HDF5, EIGEN, or HTS below to any value to disable compilation of bundled code
HDF5 ?= install
EIGEN ?= install
HTS ?= install
MINIMAP2 ?= install
SLOW5LIB ?= install
MACHINE := $(shell gcc -dumpmachine)
# when building on MacOS we only support gcc, but need to set some paths
ifneq (,$(findstring apple,$(MACHINE)))
SDK := $(shell xcrun --sdk macosx --show-sdk-path)
MAC_FLAGS = -isysroot $(SDK) -L/usr/lib
MAC=1
CXXFLAGS += $(MAC_FLAGS)
CFLAGS += $(MAC_FLAGS)
endif
ARM=0
# set an ARM-specific flag
ifneq (,$(findstring arm64,$(MACHINE)))
ARM=1
endif
# set an ARM-specific flag
ifneq (,$(findstring aarch64,$(MACHINE)))
ARM=1
endif
ifeq ($(MAC), 1)
HDF5_VERSION ?= 1.13.0
else
HDF5_VERSION ?= 1.8.14
endif
EIGEN_VERSION ?= 3.3.7
# Check operating system, OSX doesn't have -lrt
UNAME_S := $(shell uname -s)
ifeq ($(UNAME_S),Linux)
LIBS += -lrt
endif
# Default to automatically installing hdf5
ifeq ($(HDF5), install)
H5_LIB = ./lib/libhdf5.a
H5_INCLUDE = -I./include
LIBS += -ldl
else
# Use system-wide hdf5
H5_LIB =
H5_INCLUDE ?=
LIBS += -lhdf5
endif
# Default to automatically installing EIGEN
ifeq ($(EIGEN), install)
EIGEN_CHECK = eigen/INSTALL
EIGEN_INCLUDE = -I./eigen/
else
# Use system-wide eigen
EIGEN_CHECK =
EIGEN_INCLUDE ?=
endif
# Default to build and link the libhts submodule
ifeq ($(HTS), install)
HTS_LIB = ./htslib/libhts.a
HTS_INCLUDE = -I./htslib
else
# Use system-wide htslib
HTS_LIB =
HTS_INCLUDE ?=
LIBS += -lhts
endif
# Default to build and link the libminimap2 submodule
ifeq ($(MINIMAP2), install)
MINIMAP2_LIB ?= ./minimap2/libminimap2.a
MINIMAP2_INCLUDE ?= -I./minimap2
else
MINIMAP2_INCLUDE ?= -I/usr/include/minimap2
ifeq ($(MINIMAP2), static)
MINIMAP2_LIB ?= /usr/lib/libminimap2.a
else
MINIMAP2_LIB ?=
LIBS += -lminimap2
endif
endif
# Default to build and link slow5 submodule
ifeq ($(SLOW5LIB), install)
SLOW5LIB_LIB = ./slow5lib/lib/libslow5.a
SLOW5LIB_INCLUDE = -I./slow5lib/include/
else
SLOW5LIB_LIB ?=
LIBS += -lslow5 -lstreamvbyte
endif
ifeq ($(ARM), 1)
MINIMAP2_OPT += arm_neon=1
endif
# Include the src subdirectories
NP_INCLUDE = $(addprefix -I./, $(SUBDIRS))
# Add include flags
CPPFLAGS += $(H5_INCLUDE) $(HTS_INCLUDE) $(MINIMAP2_INCLUDE) $(NP_INCLUDE) $(EIGEN_INCLUDE) $(SLOW5LIB_INCLUDE)
# Main programs to build
PROGRAM = nanopolish
TEST_PROGRAM = nanopolish_test
.PHONY: all
all: depend $(PROGRAM)
#
# Build libhts
#
htslib/libhts.a:
cp etc/htslib_config.h htslib/config.h
$(MAKE) -C htslib CFLAGS="$(MAC_FLAGS)" LDFLAGS="$(MAC_FLAGS)" htslib_default_libs="-lz -lm -lbz2" NONCONFIGURE_OBJS="" || exit 255
minimap2/libminimap2.a:
$(MAKE) -C minimap2 $(MINIMAP2_OPT) CFLAGS="$(MAC_FLAGS)" libminimap2.a || exit 255
slow5lib/lib/libslow5.a:
$(MAKE) -C slow5lib CFLAGS="$(MAC_FLAGS)" || exit 255
#
# If this library is a dependency the user wants HDF5 to be downloaded and built.
#
lib/libhdf5.a:
if [ ! -e hdf5-$(HDF5_VERSION).tar.gz ]; then \
version_major_minor=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$${version_major_minor}/hdf5-$(HDF5_VERSION)/src/hdf5-$(HDF5_VERSION).tar.gz; \
fi
tar -xzf hdf5-$(HDF5_VERSION).tar.gz || exit 255
cd hdf5-$(HDF5_VERSION) && \
./configure CFLAGS="$(MAC_FLAGS)" CPPFLAGS="$(MAC_FLAGS)" --enable-threadsafe --disable-hl --libdir=`pwd`/../lib --includedir=`pwd`/../include --prefix=`pwd`/.. || exit 255
$(MAKE) -C hdf5-$(HDF5_VERSION) && $(MAKE) -C hdf5-$(HDF5_VERSION) install
# Download and install eigen if not already downloaded
eigen/INSTALL:
if [ ! -e $(EIGEN_VERSION).tar.bz2 ]; then \
wget https://gitlab.com/libeigen/eigen/-/archive/$(EIGEN_VERSION)/eigen-$(EIGEN_VERSION).tar.bz2; \
fi
tar -xjf eigen-$(EIGEN_VERSION).tar.bz2 || exit 255
mv eigen-$(EIGEN_VERSION) eigen || exit 255
#
# Source files
#
# Find the source files by searching subdirectories
CPP_SRC := $(sort $(foreach dir, $(SUBDIRS), $(wildcard $(dir)/*.cpp)))
C_SRC := $(sort $(foreach dir, $(SUBDIRS), $(wildcard $(dir)/*.c)))
EXE_SRC = src/main/nanopolish.cpp src/test/nanopolish_test.cpp
# Automatically generated object names
CPP_OBJ = $(CPP_SRC:.cpp=.o)
C_OBJ = $(C_SRC:.c=.o)
# Generate dependencies
.PHONY: depend
depend: .depend
.depend: $(CPP_SRC) $(C_SRC) $(EXE_SRC) $(H5_LIB) $(EIGEN_CHECK)
rm -f ./.depend
$(CXX) $(CXXFLAGS) $(CPPFLAGS) -MM $(CPP_SRC) $(C_SRC) > ./.depend;
# Compile objects
.cpp.o:
$(CXX) -o $@ -c $(CXXFLAGS) $(CPPFLAGS) -fPIC $<
.c.o:
$(CC) -o $@ -c $(CFLAGS) $(CPPFLAGS) $(H5_INCLUDE) -fPIC $<
# Link main executable
$(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(MINIMAP2_LIB) $(H5_LIB) $(EIGEN_CHECK) $(SLOW5LIB_LIB)
$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(MINIMAP2_LIB) $(SLOW5LIB_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
# Link test executable
$(TEST_PROGRAM): src/test/nanopolish_test.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(MINIMAP2_LIB) $(H5_LIB) $(SLOW5LIB_LIB)
$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(MINIMAP2_LIB) $(SLOW5LIB_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
.PHONY: test
test: $(TEST_PROGRAM)
./$(TEST_PROGRAM)
.PHONY: clean
clean:
rm -f $(PROGRAM) $(TEST_PROGRAM) $(CPP_OBJ) $(C_OBJ) \
src/main/nanopolish.o src/test/nanopolish_test.o
|
