Makefile

HOMEL=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
BIN=$(HOMEL)//bin

ND = nicksrc
NLIB = $(ND)/libnick.a

override LDLIBS += -lm -lgsl -lopenblas -lncurses -lz $(NLIB)
override CFLAGS += -c -O3 -Wimplicit -Wimplicit-int -DHAVE_CONFIG_H -D_IOLIB=2 -I. -Inicksrc

## Harvard O2 
override CFLAGS += -I/n/app/openblas/0.3.28-gcc-14.2.0/include -I/n/app/gsl/2.8-gcc-14.2.0/include
override LDFLAGS += -L/n/app/openblas/0.3.28-gcc-14.2.0/lib -L/n/app/gsl/2.8-gcc-14.2.0/lib/ 

PROGS = histmake damagescore pullit multimerge merge_transpose 
PROGS += transpose convertf mergeit geno_single grabpars nickhash rgprune mkdeamin

all: $(ND) $(PROGS)

.PHONY: clean clobber $(ND)

$(ND):
	$(MAKE) -C $(ND) 

$(NLIB):
	$(MAKE) -C $(ND) 

histmake:  histmake.o popsubs.o admutils.o faidx.o razf.o cigsubs.o mcio.o geno.o $(NLIB)
damagescore:  damagescore.o popsubs.o admutils.o faidx.o razf.o pmdsubs.o cigsubs.o mcio.o geno.o $(NLIB)
pullit:  pullit.o popsubs.o mcio.o admutils.o pmd.o faidx.o razf.o geno.o cigsubs.o $(NLIB)
mkdeamin:  mkdeamin.o  $(NLIB)

# pullit.c, damagescore.c, and mkdeamin.c each #include "zal.c" textually, so
# make's implicit .c.o rule (keyed only on each .c file's own mtime) won't
# rebuild their objects when zal.c changes. Declare that dependency explicitly.
pullit.o damagescore.o mkdeamin.o: zal.c
multimerge: multimerge.o mcio.o admutils.o egsubs.o geno.o $(NLIB)
merge_transpose: merge_transpose.o geno.o
transpose: transpose.o geno.o
geno_single: geno_single.o geno.o
grabpars:	grabpars.o
nickhash:  nickhash.o admutils.o $(NLIB)
## h2d.o exclude.o

convertf: convertf.o mcio.o admutils.o egsubs.o h2d.o exclude.o geno.o
mergeit: mergeit.o mcio.o admutils.o egsubs.o h2d.o exclude.o geno.o
mtcount:  mtcount.o popsubs.o admutils.o faidx.o razf.o
rgprune:  rgprune.o $(NLIB)

clean:
	$(MAKE) -C $(ND) clean
	rm -f *.o 

clobber: clean
	$(MAKE) -C $(ND) clobber
	rm -f $(PROGS)

install:	all
	mkdir -p $(BIN)
	cp $(PROGS) $(BIN)
	cp fxtract $(BIN)
	cp -r script $(BIN) 

uninstall:
	rm -f $(BIN)/*