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|
# -----------------------------------------------------------------
# Makefile for PLINK
#
# Supported platforms
# Unix / Linux UNIX
# Windows WIN
# Mac MAC
# Solaris SOLARIS
#
# Compilation options
# R plugins WITH_R_PLUGINS
# Web-based version check WITH_WEBCHECK
# Ensure 32-bit binary FORCE_32BIT
# (Ignored) WITH_ZLIB
# Link to LAPACK WITH_LAPACK
# Force dynamic linking FORCE_DYNAMIC
#
# ---------------------------------------------------------------------
# Set this variable to either UNIX, MAC or WIN
SYS = UNIX
# Leave blank after "=" to disable; put "= 1" to enable
WITH_R_PLUGINS = 1
WITH_WEBCHECK = 1
FORCE_32BIT =
WITH_ZLIB = 1
WITH_LAPACK =
FORCE_DYNAMIC =
# Put C++ compiler here; Windows has it's own specific version
CXX_UNIX = g++
CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
# Any other compiler flags here ( -Wall, -g, etc)
CXXFLAGS =
# Misc
LIB_LAPACK = /usr/lib/liblapack.so.3
# --------------------------------------------------------------------
# Do not edit below this line
# --------------------------------------------------------------------
CXXFLAGS += -O3 -I.
OUTPUT = plink
# Some system specific flags
ifeq ($(SYS),WIN)
CXXFLAGS += -DWIN -static
CXX = $(CXX_WIN)
ifndef FORCE_DYNAMIC
CXXFLAGS += -static
endif
endif
ifeq ($(SYS),UNIX)
CXXFLAGS += -DUNIX
CXX = $(CXX_UNIX)
ifndef FORCE_DYNAMIC
CXXFLAGS += -static
endif
endif
ifeq ($(SYS),MAC)
CXXFLAGS += -DUNIX -Dfopen64=fopen
CXX = $(CXX_UNIX)
endif
ifeq ($(SYS),SOLARIS)
CXXFLAGS += -fast
CXXFLAGS += -xtarget=ultraT2 # specific Sun hardware (must be specified after the -fast option)
CXXFLAGS += -xdepend=no # required to fix seg fault in iropt
LIB = -lstdc++
LIB += -lgcc
LIB += -lsocket # added for socket support
LIB += -lnsl # added for network services support
CXX = $(CXX_UNIX)
endif
ifdef FORCE_32BIT
CXXFLAGS += -m32
endif
# Flags for web-based version check
ifdef WITH_WEBCHECK
ifeq ($(SYS),WIN)
LIB += -lwsock32
endif
else
CXXFLAGS += -DSKIP
endif
SRC = plink.cpp options.cpp input.cpp binput.cpp tinput.cpp genome.cpp \
helper.cpp stats.cpp filters.cpp locus.cpp multi.cpp crandom.cpp \
cluster.cpp mds.cpp output.cpp informative.cpp assoc.cpp epi.cpp \
prephap.cpp phase.cpp trio.cpp tdt.cpp sharing.cpp genepi.cpp sets.cpp \
perm.cpp mh.cpp genedrop.cpp gxe.cpp merge.cpp hotel.cpp multiple.cpp \
haploCC.cpp haploTDT.cpp poo.cpp webcheck.cpp qfam.cpp linear.cpp \
bmerge.cpp parse.cpp mishap.cpp legacy.cpp homozyg.cpp segment.cpp \
model.cpp logistic.cpp glm.cpp dcdflib.cpp elf.cpp dfam.cpp fisher.cpp \
linput.cpp sockets.cpp lookup.cpp proxy.cpp pdriver.cpp haploQTL.cpp \
haplohelper.cpp haplowindow.cpp genogroup.cpp nonfounderphasing.cpp \
clumpld.cpp genoerr.cpp em.cpp impute.cpp metaem.cpp profile.cpp \
nlist.cpp whap.cpp simul.cpp gvar.cpp cnv.cpp step.cpp greport.cpp \
flip.cpp qualscores.cpp cnvqt.cpp cfamily.cpp setscreen.cpp idhelp.cpp \
tag.cpp hapglm.cpp lookup2.cpp blox.cpp zed.cpp dosage.cpp annot.cpp \
metaanal.cpp
HDR = plink.h options.h helper.h stats.h crandom.h sets.h phase.h \
perm.h model.h linear.h logistic.h dcdflib.h ipmpar.h cdflib.h \
fisher.h sockets.h haplowindow.h genogroup.h clumpld.h nlist.h whap.h \
gvar.h cnv.h cfamily.h idhelp.h zed.h
ifdef WITH_R_PLUGINS
CXXFLAGS += -DWITH_R_PLUGINS
HDR += sisocks.h Rsrv.h Rconnection.h config.h
SRC += r.cpp Rconnection.cpp
ifeq ($(SYS),MAC)
LIB += -ldl
endif
ifeq ($(SYS),UNIX)
LIB += -ldl -lcrypt
endif
endif
ifdef WITH_ZLIB
CXXFLAGS += -DWITH_ZLIB
HDR += zfstream.h
SRC += zfstream.cpp
LIB += -lz
endif
ifdef WITH_LAPACK
CXXFLAGS += -DWITH_LAPACK
HDR += lapackf.h
SRC += lapackf.cpp
LIB += $(LIB_LAPACK)
endif
OBJ = $(SRC:.cpp=.o)
all : $(OUTPUT)
$(OUTPUT) :
$(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB)
$(OBJ) : $(HDR)
.cpp.o :
$(CXX) $(CXXFLAGS) -c $*.cpp
.SUFFIXES : .cpp .c .o $(SUFFIXES)
$(OUTPUT) : $(OBJ)
FORCE:
clean:
rm -f *.o *~
|
