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# $Id: Makefile,v 1.10 2006/05/27 21:14:03 carlk Exp carlk $
# Makefile for TransTermHP
# Usage: "make transterm" to make the main program
# "make clean" removes all results of the compilation
# "make no_obj" removes all the .o files
VER=2.09
# files used for the main transterm program
OBJ = seq.o \
distr.o \
util.o \
map-output.o \
gene-reader.o \
search.o \
conf.o \
ermolaeva-score.o \
ermolaeva-oldconf.o \
analysis.o \
anti.o \
transterm.o
# files used for the 2ndscore program
SECONDARY_OBJ = seq.o \
search.o \
ermolaeva-score.o \
util.o \
2ndscore.o
# files to include in the distribution (.cc and .h are included automatically)
OTHERFILES = USAGE.txt \
expterm.dat \
LICENSE.txt \
RELEASE-NOTES.txt \
calibrate.sh \
random_fasta.py \
make_expterm.py \
mfold_rna.sh \
Makefile
# These options are for GCC/G++ --- you may have to change them if you
# use a different compiler
CXXFLAGS+= -g -O3 -Wall -pedantic
all: transterm 2ndscore
transterm: $(OBJ)
$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
2ndscore: $(SECONDARY_OBJ)
$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
clean: no_obj
rm -f transterm 2ndscore core.*
no_obj:
rm -f *.o
distribution:
mkdir -p transterm_hp_v$(VER)
cp $(OBJ:.o=.cc) $(SECONDARY_OBJ:.o=.cc) *.h $(OTHERFILES) transterm_hp_v$(VER)
make -C transterm_hp_v$(VER) all no_obj
test:
time ./transterm -r expterm.dat -c 0 ../test/*.{fna,ptt} > ../test/tmp.tt
-diff ../test/tmp.tt ../test/correct.tt
# DO NOT DELETE
2ndscore.o: seq.h util.h ermolaeva-score.h
2ndscore.o: search.h
analysis.o: map-output.h seq.h conf.h distr.h util.h ermolaeva-score.h
analysis.o: transterm.h
anti.o: conf.h distr.h seq.h transterm.h
conf.o: transterm.h seq.h distr.h conf.h
distr.o: distr.h
ermolaeva-oldconf.o: seq.h conf.h distr.h util.h
ermolaeva-score.o: transterm.h ermolaeva-score.h seq.h
gene-reader.o: gene-reader.h seq.h util.h
map-output.o: map-output.h seq.h conf.h distr.h util.h transterm.h
search.o: transterm.h seq.h ermolaeva-score.h util.h
seq.o: seq.h util.h
transterm.o: transterm.h seq.h util.h map-output.h
transterm.o: conf.h distr.h gene-reader.h analysis.h ermolaeva-score.h
util.o: util.h
conf.o: distr.h seq.h
ermolaeva-score.o: seq.h
gene-reader.o: seq.h
map-output.o: seq.h conf.h distr.h
search.o: seq.h
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