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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} -fPIC
cppflags += -I${sonLibPath} -fPIC
basicLibs = ${sonLibPath}/sonLib.a ${sonLibPath}/cuTest.a
basicLibsDependencies = ${basicLibs}
# 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
#
# phyloP support
#
phyloPcppflags =
phyloPlibs =
ifdef ENABLE_PHYLOP
ifndef TARGETOS
TARGETOS := $(shell uname -s)
endif
# Local Linux install (phast and clapack sister dirs to hal/)
# (note CLAPACKPATH not needed in Mac)
PHAST=../../phast
CLAPACKPATH=../../clapack
# Melissa's version of the above
# PHAST=/home/mt269/phast
# CLAPACKPATH=/usr/local/software/CLAPACK
ifeq ($(TARGETOS), Darwin)
phyloPcppflags += -DENABLE_PHYLOP -I${PHAST}/include -I${PHAST}/src/lib/pcre -framework vecLib -DVECLIB
phyloPlibs += -L${PHAST}/lib -lphast -lc
else
F2CPATH=${CLAPACKPATH}/F2CLIBS
phyloPcppflags += -DENABLE_PHYLOP -I${PHAST}/include -I${PHAST}/src/lib/pcre -I${CLAPACKPATH}/INCLUDE -I${F2CPATH}
phyloPlibs += -L${PHAST}/lib -lphast -L${CLAPACKPATH} -L${F2CPATH} -llapack -ltmg -lblaswr -lf2c
endif
endif