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Makefile
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Makefile
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# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
# Should we use the standard system zlib and libbz2?
USE_SYSTEM_ZLIB ?= false
USE_SYSTEM_LIBBZ2 ?= false
# Profile?
# Set this variable to true if you wish to profile the codes.
WANT_PROFILING=false
# Which profiling tool to use?
# Assuming you have TAU installed and setup properly,
# you can instrument codes with it to get detailed multi-threaded profiling.
# Otherwise, gprof is able to give you some information without threading info.
# Choose one of: gprof, TAU
PROFILER_OF_CHOICE=gprof
# Perform extra sanity checking?
# Set this variable to true
# if you wish the codes to perform extra sanity checking
# (to the possible detriment of performance).
WANT_EXTRA_SANITY_CHECKING=false
# Compile with debugging symbols?
# Set this variable to true
# if you wish the codes to be built with debugging symbols
# (increases code size
# and does not always produce accurate stepping in a debugger
# when optimization is turned on).
WANT_DEBUGGING=false
PREFIX=/usr/local
### NOTE: No user-serviceable parts below this line! ###
INCLUDES= -I ../third-party/seqan/core/include/ \
-I ../third-party/smhasher/
ifeq ($(USE_SYSTEM_ZLIB), false)
INCLUDES += -I ../third-party/zlib/
endif
ifeq ($(USE_SYSTEM_LIBBZ2), false)
INCLUDES += -I ../third-party/bzip2/
endif
# Warnings in common to C and C++
WARNINGS=-Wall
# Flags in common to C and C++
COMMON_FLAGS=-O3 -fPIC
SEQAN_FLAGS=-DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1
# Base C/CXXFLAGS
CPPFLAGS ?=
CPPFLAGS += $(SEQAN_FLAGS)
CXXFLAGS ?=
CXXFLAGS += $(COMMON_FLAGS) $(WARNINGS)
CXXFLAGS += -Wstrict-null-sentinel -std=c++11
CXXFLAGS += $(INCLUDES) $(CPPFLAGS)
CFLAGS ?=
CXXFLAGS += $(COMMON_FLAGS) $(WARNINGS)
CFLAGS += -Wshadow -Wcast-align -Wstrict-prototypes
CFLAGS += $(INCLUDES) $(CPPFLAGS)
LDFLAGS ?=
ifneq ($(USE_SYSTEM_ZLIB), false)
LDFLAGS += -lz
endif
ifneq ($(USE_SYSTEM_LIBBZ2), false)
LDFLAGS += -lbz2
endif
ifeq ($(WANT_DEBUGGING), true)
DEBUG_FLAGS=-g
CXXFLAGS += $(DEBUG_FLAGS)
CFLAGS += $(DEBUG_FLAGS)
endif
ifeq ($(WANT_EXTRA_SANITY_CHECKING), true)
DEFINE_KHMER_EXTRA_SANITY_CHECKS=-DKHMER_EXTRA_SANITY_CHECKS
CXXFLAGS += $(DEFINE_KHMER_EXTRA_SANITY_CHECKS)
CFLAGS += $(DEFINE_KHMER_EXTRA_SANITY_CHECKS)
endif
ifeq ($(WANT_PROFILING), true)
ifeq ($(PROFILER_OF_CHOICE), TAU)
CXX=tau_cxx.sh
endif
ifeq ($(PROFILER_OF_CHOICE), gprof)
CXXFLAGS += -pg
CFLAGS += -pg
LDFLAGS += -pg
endif
endif
# Place POSIX threads last in linking order, if needed.
ifneq ($(shell uname), Linux)
LDFLAGS += -pthread
endif
HAVE_OPENMP=$(shell \
$(CXX) -fopenmp -o chkomp .check_openmp.cc \
2>/dev/null && echo true || echo false; \
rm -f chkomp)
ifeq ($(HAVE_OPENMP), true)
CXXFLAGS +=-fopenmp
CFLAGS +=-fopenmp
endif
ifneq ($(PACKAGE_VERSION),)
VERSION = $(PACKAGE_VERSION)
else
VERSION = $(./setup.py version | grep Version | awk '{print $2}')
endif
# The ABI version of liboxli
LIB_VERSION = 1
ifeq ($(shell uname), Darwin)
SHARED_EXT = dylib
SONAME = liboxli.$(SHARED_EXT).$(LIB_VERSION)
SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) \
-compatibility_version $(LIB_VERSION) \
-current_version $(LIB_VERSION)
else
SHARED_EXT = so
SONAME = liboxli.$(SHARED_EXT).$(LIB_VERSION)
SONAME_FLAGS = -Wl,-soname=$(SONAME)
endif
LIBKHMERSO=$(SONAME)
CXXFLAGS += -DVERSION=$(VERSION)
NO_UNIQUE_RC=0
CXXFLAGS += -DNO_UNIQUE_RC=$(NO_UNIQUE_RC)
CFLAGS += -DNO_UNIQUE_RC=$(NO_UNIQUE_RC)
export CXX
export CFLAGS
export CXXFLAGS
export LDFLAGS
export VERSION
#### Third party dependencies ####
# ZLIB, use .lo not .o, so we get -fPIC and other library-related flags
ZLIB_DIR=../third-party/zlib
ZLIB_OBJS_BASE=\
adler32.lo \
crc32.lo \
deflate.lo \
infback.lo \
inffast.lo \
inflate.lo \
inftrees.lo \
trees.lo \
zutil.lo \
compress.lo \
uncompr.lo \
gzclose.lo \
gzlib.lo \
gzread.lo \
gzwrite.lo
ZLIB_OBJS=$(addprefix $(ZLIB_DIR)/, $(ZLIB_OBJS_BASE))
# BZ2
BZIP2_DIR=../third-party/bzip2
BZIP2_OBJS_BASE= \
blocksort.o \
huffman.o \
crctable.o \
randtable.o \
compress.o \
decompress.o \
bzlib.o
BZIP2_OBJS=$(addprefix $(BZIP2_DIR)/, $(BZIP2_OBJS_BASE))
#### oxli proper below here ####
LIBKHMER_OBJS= \
hashtable.o \
hashgraph.o \
hllcounter.o \
kmer_hash.o \
labelhash.o \
traversal.o \
read_aligner.o \
read_parsers.o \
subset.o \
kmer_filters.o \
assembler.o \
alphabets.o \
murmur3.o \
storage.o
PRECOMILE_OBJS ?=
PRECLEAN_TARGS ?=
ifeq ($(USE_SYSTEM_ZLIB), false)
LIBKHMER_OBJS += $(ZLIB_OBJS)
PRECOMILE_OBJS += $(ZLIB_OBJS)
PRECLEAN_TARGS += zlibclean
endif
ifeq ($(USE_SYSTEM_LIBBZ2), false)
LIBKHMER_OBJS += $(BZIP2_OBJS)
PRECOMILE_OBJS += $(BZIP2_OBJS)
PRECLEAN_TARGS += libbz2clean
endif
KHMER_HEADERS= \
hashtable.hh \
hllcounter.hh \
khmer_exception.hh \
khmer.hh \
kmer_hash.hh \
labelhash.hh \
traversal.hh \
read_aligner.hh \
read_parsers.hh \
subset.hh \
kmer_filters.hh \
assembler.hh \
alphabets.hh \
storage.hh
# START OF RULES #
# The all rule comes first!
all: $(LIBKHMERSO) liboxli.a oxli.pc
zlibclean:
(cd $(ZLIB_DIR) && make distclean)
libbz2clean:
(cd $(BZIP2_DIR) && make -f Makefile-libbz2_so clean)
clean: $(PRECLEAN_TARGS)
rm -f *.o *.a *.$(SHARED_EXT)* oxli.pc $(TEST_PROGS)
install: $(LIBKHMERSO) liboxli.a oxli.pc $(KHMER_HEADERS)
mkdir -p $(PREFIX)/lib $(PREFIX)/lib/pkgconfig $(PREFIX)/include/oxli
cp -r $(KHMER_HEADERS) \
../third-party/smhasher/MurmurHash3.h \
$(PREFIX)/include/oxli/
cp oxli.pc $(PREFIX)/lib/pkgconfig/
cp $(LIBKHMERSO) liboxli.a $(PREFIX)/lib
ln -sf $(PREFIX)/lib/$(LIBKHMERSO) $(PREFIX)/lib/liboxli.$(SHARED_EXT)
oxli.pc: oxli.pc.in
sed -e 's,@prefix@,$(PREFIX),' -e 's,@VERSION@,$(VERSION),' $< >$@
$(ZLIB_OBJS):
(cd $(ZLIB_DIR) && ./configure && make $(ZLIB_OBJS_BASE))
$(BZIP2_OBJS):
(cd $(BZIP2_DIR) && make -f Makefile-libbz2_so $(BZIP2_OBJS_BASE))
# MurMur3
murmur3.o: ../third-party/smhasher/MurmurHash3.cc
$(CXX) $(CXXFLAGS) -c -o $@ $<
%.o: %.cc $(PRECOMILE_OBJS) $(KHMER_HEADERS)
$(CXX) $(CXXFLAGS) $(LDFLAGS) -c -o $@ $<
$(LIBKHMERSO): $(LIBKHMER_OBJS)
$(CXX) $(CXXFLAGS) $(LDFLAGS) $(SONAME_FLAGS) -shared -o $@ $^
ln -sf $(SONAME) liboxli.$(SHARED_EXT)
liboxli.a: $(LIBKHMER_OBJS)
ar rcs $@ $^
ranlib $@