/
include.mk
41 lines (33 loc) · 1.21 KB
/
include.mk
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#Location of sonLib
binPath=${rootPath}bin/
libPath=${rootPath}lib/
#Modify this variable to set the location of sonLib
#(sonlib is used only for cuTest at this potin)
sonLibRootPath=${rootPath}/../sonLib
sonLibPath=${sonLibRootPath}/lib
include ${sonLibRootPath}/include.mk
dataSetsPath=/Users/hickey/Documents/Devel/genomes/datasets
cflags += -I${sonLibPath}
cppflags += -I${sonLibPath}
basicLibs = ${sonLibPath}/sonLib.a ${sonLibPath}/cuTest.a
basicLibsDependencies = ${sonLibPath}/cuTest.a
# hdf5 compilation is done through its wrappers.
# we can speficy our own (sonlib) compilers with these variables:
HDF5_CXX = ${cpp}
HDF5_CXXLINKER = ${cpp}
HDF5_CC = ${cxx}
HDF5_CCLINKER = ${cxx}
cpp = h5c++ ${h5prefix}
cxx = h5cc ${h5prefix}
# add compiler flag and kent paths if udc is enabled
# relies on KENTSRC containing path to top level kent/ dir
# and MACHTYPE being specified
ifdef ENABLE_UDC
# Find samtabix as in kent/src/inc/common.mk:
ifeq (${SAMTABIXDIR},)
SAMTABIXDIR = /hive/data/outside/samtabix/${MACHTYPE}
endif
cppflags += -DENABLE_UDC -I${KENTSRC}/src/inc -pthread
cflags += -I${KENTSRC}/src/inc -pthread
basicLibs += ${KENTSRC}/src/lib/${MACHTYPE}/jkweb.a ${SAMTABIXDIR}/libsamtabix.a -lssl -lcrypto
endif