
####### Automatic Configuration

#system
SYSTEM_SUFFIX = _linux-gnu
PREFIX=/opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold

# programms
#CXX = /opt/conda/conda-bld/bellmans-gapc_1594281223562/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ 
#CC = /opt/conda/conda-bld/bellmans-gapc_1594281223562/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc 
LD = $(CC)
LEX = /opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flex
YACC = /opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/bison
SED = sed
INSTALL = /usr/bin/install -c
SHELL = /bin/sh
HG = 

#flags
# c
CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=/opt/conda/conda-bld/bellmans-gapc_1594281223562/work=/usr/local/src/conda/bellmans-gapc-2020.07.07 -fdebug-prefix-map=/opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold=/usr/local/src/conda-prefix -O3  -std=c11 

#c++
CXXFLAGS = -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=/opt/conda/conda-bld/bellmans-gapc_1594281223562/work=/usr/local/src/conda/bellmans-gapc-2020.07.07 -fdebug-prefix-map=/opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold=/usr/local/src/conda-prefix -O3  -std=c++17 -D_XOPEN_SOURCE=500 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses

#library
SO_SUFFIX = .so
SHARED_FLAGS = -shared 
FAST_MATH =  -ffast-math 
PIC_FLAGS = -fPIC
INSTALL_SHARED_FLAG=

#bison
BISON_VERSION_FLAG =  -DBISONNEW 

#boost
BOOST_CPPFLAGS = 
BOOST_LDFLAGS = -L/opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/
BOOST_PROGRAM_OPTIONS_LIB = -lboost_program_options
BOOST_UNIT_TEST_FRAMEWORK_LIB = -lboost_unit_test_framework

#gsl
GSL_LIBS = -L/opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -lgsl -lgslcblas -lm
GSL_CFLAGS = -I/opt/conda/conda-bld/bellmans-gapc_1594281223562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include

# openmp
CXXFLAGS_OPENMP = -fopenmp

####### Fixed Configuration

AR = ar

#preprocessor
LIB_RT = rtlib
LIB_RNA = librna
LIB_GENERAL = 
INCLUDE_PATH=/include
CPPFLAGS += $(BOOST_CPPFLAGS) \
	 $(CPPFLAGS_EXTRA) \
	 $(RTLIB_CPPFLAGS)

# c
CFLAGS += -DNDEBUG

# c++
CXXFLAGS += -DNDEBUG $(BISON_VERSION_FLAG) $(CXXFLAGS_EXTRA)

# linker
LIB_PATH=/lib
LDFLAGS = $(BOOST_LDFLAGS)  \
	$(LDFLAGS_EXTRA) \
	$(RTLIB_LDFLAGS) \
	$(shell echo " $(BOOST_LDFLAGS) " | sed -e 's/[ ][ ]*[^ ]*\.o[ ]//g' | sed -e 's/\-L/-Xlinker -rpath -Xlinker /g') \
	$(shell echo " $(LDFLAGS_EXTRA) " | sed -e 's/[ ][ ]*[^ ]*\.o[ ]//g' | sed -e 's/\-L/-Xlinker -rpath -Xlinker /g') \
	$(shell echo " $(RTLIB_LDFLAGS) " | sed -e 's/[ ][ ]*[^ ]*\.o[ ]//g' | sed -e 's/\-L/-Xlinker -rpath -Xlinker /g') 

LDLIBS = $(RTLIB_LDLIBS) \
	 $(LDLIBS_EXTRA)



# Options for compling GapC generated code
# set to RTLIB_LDLIBS
RT_LDLIBS = $(GSL_LIBS) -lrna
# set to RTLIB_LDFLAGS
RT_LDFLAGS = -L$(PREFIX)$(LIB_PATH)/$(LIB_GENERAL) \
	-L$(PREFIX)$(LIB_PATH)/$(LIB_RT)  \
	-L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) \
# set to RTLIB_CPPFLAGS
RT_CPPFLAGS = $(GSL_CFLAGS) \
	 -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_GENERAL) \
	 -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_RT) \
	 -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_RNA) \

RTLIB = $(PREFIX)$(INCLUDE_PATH)/$(LIB_RT)







