Makefile.in

# @configure_input@

# Package-specific substitution variables
package = @PACKAGE_NAME@
version = @PACKAGE_VERSION@
tarname = @PACKAGE_TARNAME@
distdir = $(tarname)-$(version)
# Prefix-specific substitution variables
prefix = @prefix@
exec_prefix = @exec_prefix@
bindir = @bindir@
# VPATH-related substitution variables
srcdir = @srcdir@
VPATH = @srcdir@

ACLOCAL_AMFLAGS = -I m4 --install

all test install uninstall pprinseqc: README.md
	cd src && $(MAKE) $@
	
static:
	cd src && $(MAKE) clean && $(MAKE) CXXFLAGS='-static -std=c++11 -Wall -O3 -pthread -lboost_filesystem -lboost_system  -lboost_iostreams -lz' && mv prinseq++ .. && $(MAKE) clean
	tar cvzf  binary_$(distdir).tar.gz prinseq++
	rm prinseq++

clean : FORCE
	cd src && $(MAKE) $@
	-rm -rf $(distdir).tar.gz html latex binary_$(distdir).tar.gz prinseq++ contigs.fasta
	
clear : clean	

cleandist : FORCE
	cd src && $(MAKE) clean
	-rm -rf autom4te.cache 
	-rm -f config.h config.log aclocal.m4 config.log config.status configure install-sh Makefile config.guess config.sub README.md
	-rm -rf $(distdir).tar.gz html latex binary_$(distdir).tar.gz prinseq++ contigs.fasta

cleardist : cleandist

dist : $(distdir).tar.gz

$(distdir).tar.gz : $(distdir)
	tar chof - $(distdir) | gzip -9 -c > $@
	rm -rf $(distdir)

$(distdir): FORCE
	mkdir -p $(distdir)/src
	cp $(srcdir)/configure.ac $(distdir)
	cp $(srcdir)/configure $(distdir)
	cp $(srcdir)/config.h.in $(distdir)
	cp $(srcdir)/install-sh $(distdir)
	cp $(srcdir)/Makefile.in $(distdir)
	cp $(srcdir)/config.sub $(distdir)
	cp $(srcdir)/config.guess $(distdir)
	cp $(srcdir)/README.md $(distdir)
	cp $(srcdir)/README.md.in $(distdir)
	cp $(srcdir)/src/Makefile.in $(distdir)/src
	cp $(srcdir)/src/main.cpp $(distdir)/src
	cp $(srcdir)/src/reads.cpp $(distdir)/src
	cp $(srcdir)/src/reads.h $(distdir)/src
	cp $(srcdir)/src/test_F.fastq $(distdir)/src
	cp $(srcdir)/src/test_R.fastq $(distdir)/src
	cp $(srcdir)/src/test_F.fastq.gz $(distdir)/src
	cp $(srcdir)/src/test_R.fastq.gz $(distdir)/src
	cp $(srcdir)/src/bloom_filter.hpp $(distdir)/src
	cp $(srcdir)/Doxyfile $(distdir)/src
	cp $(srcdir)/src/verbose.h $(distdir)/src
	cp $(srcdir)/src/verbose.cpp $(distdir)/src
	
FORCE:
	-rm -f $(distdir).tar.gz >/dev/null 2>&1
	-rm -rf $(distdir) >/dev/null 2>&1
	
release: distcheck static
	hub release create -a $(distdir).tar.gz -a binary_$(distdir).tar.gz -m "v@PACKAGE_VERSION@" "v@PACKAGE_VERSION@"

distcheck: $(distdir).tar.gz
	gzip -cd $(distdir).tar.gz | tar xvf -
	cd $(distdir) && ./configure
	cd $(distdir) && $(MAKE) all
	cd $(distdir) && $(MAKE) test
	cd $(distdir) && $(MAKE) DESTDIR=$${PWD}/_inst install
	cd $(distdir) && $(MAKE) DESTDIR=$${PWD}/_inst uninstall
	@remaining="`find $${PWD}/$(distdir)/_inst -type f | wc -l`"; \
if test "$${remaining}" -ne 0; then \
echo "*** $${remaining} file(s) remaining in stage directory!"; \
exit 1; \
	fi
	cd $(distdir) && $(MAKE) clean
	rm -rf $(distdir)
	@echo "*** Package $(distdir).tar.gz is ready for distribution."

doc: all
	doxygen Doxyfile
	cd latex && $(MAKE) && mv refman.pdf .. 

Makefile: Makefile.in config.status 
	./config.status $@
	
README.md: README.md.in config.status
	./config.status $@

config.status: configure
	./config.status --recheck


.PHONY: all clean dist FORCE check distcheck install uninstall static release cleandist clear cleardist doc