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# ======================================================================
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# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006 Whitehead
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# Institute for Biomedical Research, Steve Rozen, and Helen Skaletsky
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following disclaimer
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# in the documentation and/or other materials provided with the
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# * Neither the names of the copyright holders nor contributors may
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# be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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# ======================================================================
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# ======================================================================
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# Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
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# general users and for biologist programmers. In: Krawetz S, Misener S
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# (eds) Bioinformatics Methods and Protocols: Methods in Molecular
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# Biology. Humana Press, Totowa, NJ, pp 365-386. Source code available
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# at http://fokker.wi.mit.edu/primer3/.
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# ======================================================================
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MAX_PRIMER_LENGTH = 36
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WHITEHEAD_SPECIFIC_HACK = -include /usr/include/sys/types.h
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CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ $(WHITEHEAD_SPECIFIC_HACK)
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P_DEFINES = -DDPAL_MAX_ALIGN=$(MAX_PRIMER_LENGTH) -DMAX_PRIMER_LENGTH=$(MAX_PRIMER_LENGTH)
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CFLAGS = $(CC_OPTS) $(O_OPTS)
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# ======================================================================
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# IMPORTANT: on MacOS X and some other Unix/Linux systems where
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# static libraries are not routinely available, -static has to
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PRIMER_EXE = primer3_core
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PRIMER_OBJECTS=primer3_main.o\
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EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
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$(PRIMER_EXE): $(PRIMER_OBJECTS)
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$(CC) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
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# For use with the "testcenter" testing program (CenterLine Software
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# Inc, http://www.centerline.com)
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$(PRIMER_EXE).tc: $(PRIMER_OBJECTS) /usr/lib/debug/malloc.o
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proof $(CC) $(CFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
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ntdpal: ntdpal_main.o dpal.o
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$(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
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oligotm: oligotm_main.c oligotm.o
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$(CC) $(CFLAGS) -o $@ oligotm_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
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long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
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$(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
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boulder_input.o: boulder_input.c boulder_input.h primer3.h primer3_release.h dpal.h
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$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ boulder_input.c
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dpal.o: dpal.c dpal.h primer3_release.h
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$(CC) -c $(CFLAGS) -o $@ dpal.c
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dpal_primer.o: dpal.c dpal.h primer3_release.h
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$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
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format_output.o: format_output.c primer3_release.h format_output.h primer3.h dpal.h
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$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
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ntdpal_main.o: ntdpal_main.c dpal.h
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$(CC) -c $(CC_OPTS) -o $@ ntdpal_main.c
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# We use CC_OPTS above rather than CFLAGS because
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# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
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oligotm_main.o: oligotm_main.c oligotm.h
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$(CC) -c $(CFLAGS) -o $@ ntdpal_main.c
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oligotm.o: oligotm.c oligotm.h primer3_release.h
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primer3.o: primer3.c primer3.h primer3_release.h
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$(CC) -c $(CFLAGS) $(P_DEFINES) primer3.c
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primer3_main.o: primer3_main.c primer3.h primer3_release.h dpal.h oligotm.h format_output.h
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$(CC) -c $(CFLAGS) $(P_DEFINES) primer3_main.c
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primer_test: $(PRIMER_EXE)
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cd ../test; primer_test.pl
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src/Makefile
