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.PHONY=all
SRCDIR:=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
include ${CURDIR}/../../defines.mk
include ${SRCDIR}/../../rules.mk
# If pbbam and htslib are prebuilt and included in blasr/defines.mk,
# set PacBioBAM_INCLUDE_DIRS, HTSLIB_INCLUDE_DIRS, PacBioBAM_LIBRARIES
# and HTSLIB_LIBRARIES as below. Otherwise, just set PacBioBAM_RootDir instead.
all: ${CURDIR}/src/* ${CURDIR}/tests/src/*
@mkdir -p ${CURDIR}/build && \
cd ${CURDIR}/build && \
cmake -DBoost_INCLUDE_DIRS=${BOOST_INC} \
-DPacBioBAM_INCLUDE_DIRS=${PBBAM_INC} \
-DHTSLIB_INCLUDE_DIRS=${HTSLIB_INC} \
-DPacBioBAM_LIBRARIES=${PBBAM_LIB}/libpbbam${SH_LIB_EXT} \
-DHTSLIB_LIBRARIES=${HTSLIB_LIB}/libhts${SH_LIB_EXT} \
-DPBDATA_INCLUDE_DIRS=${LIBPBDATA_INC} \
-DPBDATA_LIBRARIES=${LIBPBDATA_LIB}/libpbdata${SH_LIB_EXT} \
-DPBIHDF_INCLUDE_DIRS=${LIBPBIHDF_INC} \
-DPBIHDF_LIBRARIES=${LIBPBIHDF_LIB}/libpbihdf${SH_LIB_EXT} \
-DBLASR_INCLUDE_DIRS=${LIBBLASR_INC}/ \
-DBLASR_LIBRARIES=${LIBBLASR_LIB}/libblasr${SH_LIB_EXT} \
-DHDF5_INCLUDE_DIRS=${HDF5_INC} \
-DHDF5_CPP_LIBRARIES=${HDF5_LIB}/libhdf5_cpp${SH_LIB_EXT} \
-DHDF5_LIBRARIES=${HDF5_LIB}/libhdf5${SH_LIB_EXT} \
-DBax2Bam_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \
../ && \
make
clean:
@rm -rf ${CURDIR}/bin/
@rm -rf ${CURDIR}/build
|
