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# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#setenv BOOST_PATH /netopt/ncbi_tools64/boost-1.62.0-ncbi1
ifdef BOOST_PATH
BOOST_INCL := -I $(BOOST_PATH)/include
BOOST_LIB := -L $(BOOST_PATH)/lib
endif
NGS_DIR := $(CURDIR)/NGS
VDB_PATH := $(NGS_DIR)/vdb_out
NGS_PATH := $(NGS_DIR)/ngs_out
BUILD_PATH := $(NGS_DIR)/build
VDB_INCL := -I $(VDB_PATH)/include
VDB_LIB := -L $(VDB_PATH)/lib64
NGS_INCL := -I $(NGS_PATH)/include
NGS_LIB := -L $(NGS_PATH)/lib64
ifeq ($(origin CXX),default)
CXX = c++
endif
CFLAGS += -std=c++11 -fdiagnostics-color=never
LDLAGS += -std=c++11 -fdiagnostics-color=never
CFLAGS += -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
-fomit-frame-pointer $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
LIBS += -lngs-c++ -lncbi-vdb -lzstd \
$(BOOST_LIB) \
-lboost_program_options \
-lboost_iostreams \
-lboost_regex \
-lboost_timer \
-lboost_chrono \
-lrt -ldl -lm -lpthread -lz
%.o: %.cpp
$(CXX) -c -o $@ $< $(CFLAGS)
binaries=skesa gfa_connector kmercounter
all: $(binaries)
.PHONY: clean
clean:
rm -f $(binaries) *.o $(NGS_DIR)/ngs.done
glb_align.o: glb_align.hpp Makefile
skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
skesa: skesa.o glb_align.o
$(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
gfa_connector.o: gfa.hpp glb_align.hpp common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp graphdigger.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile
gfa_connector: gfa_connector.o glb_align.o
$(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
kmercounter.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
kmercounter: kmercounter.o glb_align.o
$(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
$(NGS_DIR)/ngs.done:
rm -fr $(NGS_DIR)
mkdir -p $(NGS_DIR)/ngs
mkdir $(BUILD_PATH)
mkdir $(NGS_PATH)
mkdir $(VDB_PATH)
cd $(NGS_DIR)/ngs; git init; git remote add -f origin https://github.com/ncbi/ngs.git; git config core.sparseCheckout true; echo "ngs-sdk" >> .git/info/sparse-checkout; git pull origin master
cd $(NGS_DIR)/ngs/ngs-sdk; ./configure --prefix=$(NGS_PATH) --build-prefix=$(BUILD_PATH); make; make install
cd $(NGS_DIR); git clone https://github.com/ncbi/ncbi-vdb.git
cd $(NGS_DIR)/ncbi-vdb; ./configure --prefix=$(VDB_PATH) --build-prefix=$(BUILD_PATH); make; make install
touch $@
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