# Simple Makefile for Glimmer3
BINDIR = ../bin
OBJDIR = ../obj
LIBDIR = ../lib
VPATH = $(BINDIR):$(OBJDIR):$(LIBDIR)
COMMON_SRCS = delcher.cc fasta.cc gene.cc
COMMON_OBJS = $(COMMON_SRCS:.cc=.o)
GLIMMER_SRCS = anomaly.cc glimmer3.cc long-orfs.cc test.cc
GLIMMER_OBJS = $(GLIMMER_SRCS:.cc=.o)
GLIMMER_PROGS = $(GLIMMER_SRCS:.cc=)
ICM_SRCS = icm.cc build-icm.cc build-fixed.cc score-fixed.cc
ICM_OBJS = $(ICM_SRCS:.cc=.o)
ICM_PROGS = build-icm build-fixed score-fixed
UTIL_SRCS = entropy-profile.cc entropy-score.cc extract.cc multi-extract.cc \
start-codon-distrib.cc uncovered.cc window-acgt.cc
UTIL_OBJS = $(UTIL_SRCS:.cc=.o)
UTIL_PROGS = $(UTIL_SRCS:.cc=)
SOURCES = $(COMMON_SRCS) $(GLIMMER_SRCS) $(ICM_SRCS) $(UTIL_SRCS)
OBJECTS = $(COMMON_OBJS) $(GLIMMER_OBJS) $(ICM_OBJS) $(UTIL_OBJS)
PROGS = $(COMMON_PROGS) $(GLIMMER_PROGS) $(ICM_PROGS) $(UTIL_PROGS)
LIBRARIES = libGLMcommon.a libGLMicm.a
AR = ar
ARFLAGS = -rsv
CPPC = g++
CFLAGS = -g
LDFLAGS = -lm -L $(LIBDIR)
DEPEND_FILES = *.cc *.hh
CLEANABLE_FILES = $(OBJDIR)/*.o *~
ALL = $(LIBRARIES) $(PROGS)
.SUFFIXES: .cc
.cc.o:
$(CPPC) $(CFLAGS) -c $*.cc -o $(OBJDIR)/$*.o
all: $(ALL)
anomaly: anomaly.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/anomaly.o $(LDFLAGS) -lGLMcommon
build-fixed: build-fixed.o libGLMicm.a libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/build-fixed.o $(LDFLAGS) -lGLMicm -lGLMcommon
build-icm: build-icm.o libGLMicm.a libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/build-icm.o $(LDFLAGS) -lGLMicm -lGLMcommon
entropy-profile: entropy-profile.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/entropy-profile.o $(LDFLAGS) -lGLMcommon
entropy-score: entropy-score.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/entropy-score.o $(LDFLAGS) -lGLMcommon
extract: extract.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/extract.o $(LDFLAGS) -lGLMcommon
glimmer3: glimmer3.o libGLMicm.a libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/glimmer3.o $(LDFLAGS) -lGLMicm -lGLMcommon
long-orfs: long-orfs.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/long-orfs.o $(LDFLAGS) -lGLMcommon
multi-extract: multi-extract.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/multi-extract.o $(LDFLAGS) -lGLMcommon
score-fixed: score-fixed.o libGLMicm.a libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/score-fixed.o $(LDFLAGS) -lGLMicm -lGLMcommon
start-codon-distrib: start-codon-distrib.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/start-codon-distrib.o $(LDFLAGS) -lGLMcommon
test: test.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/test.o $(LDFLAGS) -lGLMcommon
uncovered: uncovered.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/uncovered.o $(LDFLAGS) -lGLMcommon
window-acgt: window-acgt.o libGLMcommon.a
$(CPPC) -o $(BINDIR)/$@ $(OBJDIR)/window-acgt.o $(LDFLAGS) -lGLMcommon
libGLMcommon.a: $(COMMON_OBJS)
$(AR) $(ARFLAGS) $(LIBDIR)/$@ $(OBJDIR)/delcher.o $(OBJDIR)/fasta.o $(OBJDIR)/gene.o
libGLMicm.a: icm.o
$(AR) $(ARFLAGS) $(LIBDIR)/$@ $(OBJDIR)/icm.o
depend:
makedepend $(DEPEND_FILES)
clean:
/bin/rm -f $(CLEANABLE_FILES)
# DO NOT DELETE THIS LINE -- make depend depends on it.