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all:
SRCDIR:=$(dir $(realpath $(firstword $(MAKEFILE_LIST))))
-include ${CURDIR}/defines.mk
-include ${SRCDIR}/rules.mk
foo:
echo $(realpath $(firstword $(MAKEFILE_LIST)))
echo $(firstword $(MAKEFILE_LIST))
echo $(MAKEFILE_LIST)
echo ${SRCDIR}
GET_SHA1 := $(shell git -C ${SRCDIR} describe --always --dirty='*')
CXXFLAGS += -O3 -g -DSHA1_7=\"${GET_SHA1}\"
CXXOPTS += \
-std=c++0x -pedantic \
-Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual \
-MMD -MP
GCXXFLAGS := -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
override CXXFLAGS += ${CXXOPTS} ${GCXXFLAGS}
#INC_DIRS:=${LIBBLASR_INC} ${LIBPBIHDF_INC} ${LIBPBDATA_INC} ${PBBAM_INC} ${HTSLIB_INC} ${HDF5_INC} ${ZLIB_INC}
#LIB_DIRS:=${LIBBLASR_LIB} ${LIBPBIHDF_LIB} ${LIBPBDATA_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${HDF5_LIB} ${ZLIB_LIB}
#LDLIBS := \
# ${LIBBLASR_LIBFLAGS} ${LIBPBIHDF_LIBFLAGS} ${LIBPBDATA_LIBFLAGS} \
# ${PBBAM_LIBFLAGS} ${HTSLIB_LIBFLAGS} ${HDF5_LIBFLAGS} ${ZLIB_LIBFLAGS} \
# -ldl -lpthread
# HDF5 needs -ldl, but mobs does not pass it in.
SRCS := Blasr.cpp
OBJS := ${SRCS:.cpp=.o}
DEPS := ${SRCS:.cpp=.d}
override BLASR_PATH=${SRCDIR}/
export BLASR_PATH
override LD_LIBRARY_PATH:=${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}:${HDF5_LIB}:${HTSLIB_LIB}:${PBBAM_LIB}:${ZLIB_LIB}:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
# Note: On macosx, this would be DYLD_LIBRARY_PATH.
vpath %.cpp ${SRCDIR}
init-submodule:
${MAKE} update-submodule
${MAKE} configure-submodule
${MAKE} build-submodule
update-submodule:
git submodule update --init
configure-submodule:
${MAKE} -f ${SRCDIR}/sub.mk configure-submodule
build-submodule:
${MAKE} -C libcpp
distclean-submodule:
${RM} -r libcpp
# The rules above must be run separately.
all: blasr makeutils
#all: makeextrautils #This would require pbbam.
blasr: ${OBJS}
${CXX} -o $@ ${CXXFLAGS} ${CPPFLAGS} -MF"${@:%=%.d}" ${OBJS} ${LDFLAGS} ${LDLIBS}
@echo LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
makeutils:
${MAKE} -C utils
makeextrautils:
${MAKE} -C extrautils
cramtests: blasr utils
${MAKE} -f cram.mk cramtests
${MAKE} -C utils cramtests
cramfast: blasr utils
${MAKE} -f cram.mk cramfast
${MAKE} -C utils cramfast
crammild: blasr utils
${MAKE} -f cram.mk crammild
${MAKE} -C utils crammild
gtest: blasr
# This requires the submodule to be configured with gtest.
${MAKE} -C libcpp gtest
check: gtest cramtests
cleanall: cleanlib clean
# cleanlib is only for submodule users
cleanlib: libcpp/defines.mk
${MAKE} -C libcpp clean
clean:
${RM} blasr ${OBJS} ${DEPS} blasr.d
${MAKE} -C utils clean
${MAKE} -C extrautils clean
-include ${DEPS}
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