Makefile

# Makefile for Nonpareil
# @update Dec 16 2013
# @author Luis M. Rodriguez-R <lmrodriguez at gmail dot com>

include globals.mk

enveomics=enveomics/
universal=$(enveomics)universal.o
sqlite=$(enveomics)sqlite.o -lsqlite3
regex=$(enveomics)regex.o
go=$(enveomics)go.o $(regex) $(sqlite)
sequence=$(enveomics)sequence.o
multinode=$(enveomics)multinode.o
seqreader=$(enveomics)SeqReader.o
references=$(enveomics)References.o
hash=$(enveomics)Hash.o
kmercounter=$(enveomics)KmerCounter.o
ldflags=-lpthread -lz
np_objs=$(universal) $(multinode) $(sequence) $(seqreader) $(reader) $(kmercounter) $(references) $(hash) $(enveomics)nonpareil_mating.o $(enveomics)nonpareil_sampling.o


all:	clean nonpareil nonpareil-mpi test release

enveomics:
	cd $(enveomics) && $(MAKE) all

nonpareil-mpi:
	cd $(enveomics) && $(MAKE) $@
	$(mpicpp) nonpareil.cpp $(np_objs) $(ldflags) $(mpiflags) $(CPPFLAGS) -o $@

nonpareil:
	cd $(enveomics) && $(MAKE) $@
	$(cpp) nonpareil.cpp $(np_objs) $(ldflags) $(CPPFLAGS) -o $@

nuc_sampler:
	cd $(enveomics) && $(MAKE) sequence
	$(cpp) nuc_sampler.cpp $(universal) $(sequence) $(ldflags) $(CPPFLAGS) -o nuc_sampler

clean:
	cd $(enveomics) && $(MAKE) clean
	rm -f test/test.*.enve-* test/test.fast[aq] test/DELETE.np* nonpareil.np*

install:
	if [ ! -d $(bindir) ] ; then mkdir -p $(bindir) ; fi
	if [ ! -d $(mandir) ] ; then mkdir -p $(mandir) ; fi
	if [ -e nonpareil ] ; then install -m 0755 nonpareil $(bindir)/ ; fi
	if [ -e nonpareil-mpi ] ; then install -m 0755 nonpareil-mpi $(bindir)/ ; fi
	cp docs/_build/man/nonpareil.1 $(mandir)/nonpareil.1
	$(R) CMD INSTALL utils/Nonpareil

test: nonpareil
	./test.bash

release: nonpareil
	$(eval release=$(shell ./nonpareil -V | perl -pe 's/.*v//'))
	$(eval version=$(shell echo $(release) | perl -pe 's/\.[^\.]+$$//'))
	sed -i '' "s/^\(version = \)'.*'$$/\1'$(version)'/" docs/conf.py
	sed -i '' "s/^\(release = \)'.*'$$/\1'$(release)'/" docs/conf.py
	sed -i '' "s/^\(copyright = u'2013-\)[0-9]*/\1$(shell date +%Y)/" docs/conf.py
	cd docs && $(MAKE) man
	cp nonpareil binaries/MacOSX_Intel/nonpareil-$(release)
	cp nonpareil-mpi binaries/MacOSX_Intel/nonpareil-mpi-$(release)

.PHONY: all clean install test release