makefile.linux

mfold

# Makefile for mfold version 3.2
# Michael Zuker, June 2005 
# Rensselaer Polytechnic Institute
# Copyright Washington University School of Medicine 1998-
SHELL	= /bin/sh

# Set optimization flags as high as possible. What you see below is
# only a guide.
# Must choose 1 definition for FFLAGS and CFLAGS or make up your own
#FFLAGS	= -O3 -col120 -static -mips4 # SGI with mips4
#FFLAGS	= -O3 -col120 -static -mips2 # SGI with mips2
FFLAGS	= -O3 -C -fno-automatic -ffixed-line-length-none # gnu Fortran
#FFLAGS	= -O3 -extend_source # Compaq Alpha 8400 (Tru64 Unix 4.0D)
#FFLAGS	= -Bstatic -O3 -e # Sun/Solaris (no dynamic library links)
#FFLAGS	= -O2 -e # Sun/Solaris
#CFLAGS = -O 
CFLAGS	= -O -Wno-deprecated -fomit-frame-pointer # -traditional -traditional-cpp # Solaris (Sparc and Intel), Alpha

# Define compilers as appropriate
#FTN	= f95
#FTN	= f77 
FTN	= g77
CC	= gcc
#C++	= cxx  # Compaq Alpha 8400 (Tru64 Unix 4.0D)
C++	= g++
#C++     = cpp
#C++	= c++

# Must choose 1 combination for INCL, INCL2 and BITS
#INCL	= src/rna-default.inc # "iibset" and "iibits" available (SGI, Alpha)
#INCL2	= src/rna2-default.inc
#BITS	= src/bits.f # (as above)
#INCL	= src/rna-sun.inc # Sparc/Solaris with "bis" and "bit" available
#INCL2	= src/rna2-sun.inc
#BITS	= src/bits-sun.f # (as above)
INCL	= src/rna-gnu.inc # gnu version; will run anywhere
INCL2	= src/rna2-gnu.inc
BITS	= src/bits-gnu.f # (as above)

#BINDIR	= /usr/local/bin
#DATDIR	= /usr/local/dat
#BINDIR	= /usr/local/share/bin
#DATDIR	= /usr/local/share/mfold
BINDIR	= /home/apps/bin
DATDIR	= /home/apps/share/mfold

MAXN2	= 800
#MAXN2	= 10600
#MAXN2	= 16484
MAXN	= 8000
MAXN1	= 8000

######################################################################
# Nothing below here need be edited when installing. #
######################################################################

BINEXE	= bin/distance bin/ct2bp bin/ct2rnaml bin/ct_compare bin/efn bin/efn2\
	bin/newtemp bin/scorer bin/auxgen bin/sav2plot bin/sav2p-num\
	bin/h-num.exe bin/ss-count bin/add-dHdSTm bin/nafold bin/nafold2\
	bin/quikfold bin/sav2plot2 bin/sav2p-num2 bin/add-dHdSTm2 

SCRIPTS	= bin/mfold bin/h-num bin/filter-sort bin/auto_ct2ps.sh\
	bin/reformat-seq.sh

DATA	= *.dg *.dh *.dgd *.dhd *.gif *.dat* *.awk *.html 
BINS	= $(BINEXE) $(SCRIPTS)

all: $(BINEXE) 
	strip $(BINEXE) ; chmod 755 $(BINS) 

clean:
	rm -f $(BINEXE) src/maxn*.inc src/rna.inc *.o *.u c++/*.o

install: $(BINEXE)
	cp $(BINEXE) $(SCRIPTS) $(BINDIR)
	@echo "Executables copied to $(BINDIR)"
	cd dat ; cp $(DATA) $(DATDIR) ; cd ../
	@echo "Data files copied to $(DATDIR)"
	@echo "Everything is installed. You can do a 'make clean'"

# distance

bin/distance: src/distance.f src/bpin.f src/bpsrch.f
	$(FTN) $(FFLAGS) -o bin/distance src/distance.f src/bpin.f src/bpsrch.f

# miscellaneous

bin/ct2rnaml: src/ct2rnaml.c
	$(CC) $(CFLAGS) -o bin/ct2rnaml src/ct2rnaml.c

bin/ct_compare: src/ct_compare.f
	$(FTN) $(FFLAGS) -o bin/ct_compare src/ct_compare.f

bin/ct2bp: src/ct2bp.f
	$(FTN) $(FFLAGS) -o bin/ct2bp src/ct2bp.f

bin/efn: src/efn.f src/efn.inc
	$(FTN) $(FFLAGS) -o bin/efn src/efn.f

bin/efn2: c++/efn2.cpp c++/algorithm.cpp c++/algorithm.h c++/platform.cpp
	$(C++) $(CFLAGS) -o bin/efn2 c++/efn2.cpp -lm

bin/h-num.exe: src/h-num.f
	$(FTN) $(FFLAGS) -o bin/h-num.exe src/h-num.f

bin/newtemp: src/newtemp.f src/ion.f src/dc.f
	$(FTN) $(FFLAGS) -o bin/newtemp src/ion.f src/dc.f src/newtemp.f

bin/scorer: src/scorer.f
	$(FTN) $(FFLAGS) -o bin/scorer src/scorer.f

bin/auxgen: src/auxgen.f
	$(FTN) $(FFLAGS) -o bin/auxgen src/auxgen.f

bin/sav2plot: src/sav2plot.f src/maxn.inc
	$(FTN) $(FFLAGS) -o bin/sav2plot src/sav2plot.f

bin/sav2p-num: src/sav2p-num.f src/maxn.inc
	$(FTN) $(FFLAGS) -o bin/sav2p-num src/sav2p-num.f

bin/sav2plot2: src/sav2plot2.f src/maxn2.inc
	$(FTN) $(FFLAGS) -o bin/sav2plot2 src/sav2plot2.f

bin/sav2p-num2: src/sav2p-num2.f src/maxn2.inc
	$(FTN) $(FFLAGS) -o bin/sav2p-num2 src/sav2p-num2.f

bin/ss-count: src/ss-count.f
	$(FTN) $(FFLAGS) -o bin/ss-count src/ss-count.f

bin/add-dHdSTm: src/add-dHdSTm.f
	$(FTN) $(FFLAGS) -o bin/add-dHdSTm src/add-dHdSTm.f

bin/add-dHdSTm2: src/add-dHdSTm2.f
	$(FTN) $(FFLAGS) -o bin/add-dHdSTm2 src/add-dHdSTm2.f

# nafold, quikfold

NASRC	= src/main.f src/rna.f src/misc.f src/efiles.f src/sort.f \
	src/dc.f $(BITS) src/formid.f src/multid.f

QUIK	= src/quik.f src/rna-quik.f src/misc-quik.f src/dc.f src/multid.f

bin/nafold2: $(INCL2) src/maxn2.inc $(NASRC)
	cp $(INCL2) src/rna.inc
	cp $(INCL2) src/rna_or_efn.inc
	$(FTN) $(FFLAGS) -o bin/nafold2 $(NASRC) 

bin/nafold: $(INCL) src/maxn.inc $(NASRC)
	cp $(INCL) src/rna.inc
	cp $(INCL) src/rna_or_efn.inc
	$(FTN) $(FFLAGS) -o bin/nafold $(NASRC) 

bin/quikfold: src/maxn1.inc src/maxn2.inc $(QUIK)
	$(FTN) $(FFLAGS) -o bin/quikfold $(QUIK) 

src/maxn.inc:
	echo "      parameter (maxn=$(MAXN))" > src/maxn.inc

src/maxn1.inc:
	echo "      parameter (maxn=$(MAXN1))" > src/maxn1.inc

src/maxn2.inc:
	echo "      parameter (maxn=$(MAXN2))" > src/maxn2.inc