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ROOT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
THREADS := 4
export LIBCUCKOO = -I${ROOT_DIR}/lib/libcuckoo
export INTERVAL_TREE = -I${ROOT_DIR}/lib/interval_tree
export LEMON = -I${ROOT_DIR}/lib/lemon
export BIN_DIR = ${ROOT_DIR}/bin
export MINIMAP2_DIR = ${ROOT_DIR}/lib/minimap2
export SAMTOOLS_DIR = ${ROOT_DIR}/lib/samtools-1.9
export CXXFLAGS += ${LIBCUCKOO} ${INTERVAL_TREE} ${LEMON}
export LDFLAGS += -lz -lminimap2
ifeq ($(shell uname -m),arm64)
export arm_neon=1
export aarch64=1
endif
.PHONY: clean all profile debug
.DEFAULT_GOAL := all
${BIN_DIR}/flye-minimap2:
make -C ${MINIMAP2_DIR} -j ${THREADS}
cp ${MINIMAP2_DIR}/minimap2 ${BIN_DIR}/flye-minimap2
minimap2: ${BIN_DIR}/flye-minimap2
samtools: ${BIN_DIR}/flye-samtools
${BIN_DIR}/flye-samtools:
cd ${SAMTOOLS_DIR} && ./configure --without-curses --disable-bz2 --disable-lzma --enable-plugins
make samtools -C ${SAMTOOLS_DIR} -j ${THREADS}
cp ${SAMTOOLS_DIR}/samtools ${BIN_DIR}/flye-samtools
all:
make release -C src -j ${THREADS}
profile: minimap2 samtools
make profile -C src -j ${THREADS}
debug:
make debug -C src -j ${THREADS}
clean:
make clean -C src
rm -f ${BIN_DIR}/flye-minimap2
rm -f ${BIN_DIR}/flye-samtools
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