# This can be overridden e.g.: make install INSTALL_DIR=...
INSTALL_DIR?=$(PWD)

# Guess wether to use lib or lib64
#libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
# We don't have platform specific lib stuff
libdir=lib

# Overriding this is currently not fully supported as the code won't know
# to what this is set then. You can try setting HHLIB.
INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hh
INSTALL_SCRIPTS_DIR?=$(INSTALL_LIB_DIR)/scripts
INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data
INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin

dist_name=hhsuite-2.0.16

.PHONY: all_static
all_static: ffindex_static
	$(MAKE) -C src all_static

.PHONY: all
all: ffindex
	$(MAKE) -C src all

doc:
	$(MAKE) -C src hhsuite-userguide.pdf

hhblits_static: hhblits_static
	$(MAKE) -C src hhblits_static

hhblits: ffindex
	$(MAKE) -C src all

.PHONY: ffindex
ffindex:
	$(MAKE) -C lib/ffindex

ffindex_static:
	$(MAKE) -C lib/ffindex FFINDEX_STATIC=1
	
install:
	$(MAKE) -C lib/ffindex install INSTALL_DIR=$(INSTALL_DIR)
	mkdir -p $(INSTALL_DIR)/bin
	install src/hhblits     $(INSTALL_DIR)/bin/hhblits
	install src/hhalign     $(INSTALL_DIR)/bin/hhalign
	install src/hhconsensus $(INSTALL_DIR)/bin/hhconsensus
	install src/hhfilter    $(INSTALL_DIR)/bin/hhfilter
	install src/hhmake      $(INSTALL_DIR)/bin/hhmake
	install src/hhsearch    $(INSTALL_DIR)/bin/hhsearch
	mkdir -p $(INSTALL_LIB_DIR)
	mkdir -p $(INSTALL_LIB_BIN_DIR)
	install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate
	mkdir -p $(INSTALL_DATA_DIR)
	install -m 0644 data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib
	install -m 0644 data/cs219.lib        $(INSTALL_DATA_DIR)/cs219.lib
	install -m 0644 data/do_not_delete    $(INSTALL_DATA_DIR)/do_not_delete
	install -m 0644 data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr
	install -m 0644 data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin
	install -m 0644 data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq
	mkdir -p $(INSTALL_SCRIPTS_DIR)
	install -m 0644 scripts/Align.pm        $(INSTALL_SCRIPTS_DIR)/Align.pm
	install -m 0644 scripts/HHPaths.pm      $(INSTALL_SCRIPTS_DIR)/HHPaths.pm
	install scripts/addss.pl        $(INSTALL_SCRIPTS_DIR)/addss.pl
	install scripts/create_profile_from_hhm.pl   $(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl
	install scripts/create_profile_from_hmmer.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl
	install scripts/hhmakemodel.pl $(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl
	install scripts/reformat.pl    $(INSTALL_SCRIPTS_DIR)/reformat.pl
	install scripts/splitfasta.pl    $(INSTALL_SCRIPTS_DIR)/splitfasta.pl
	install scripts/multithread.pl    $(INSTALL_SCRIPTS_DIR)/multithread.pl
	install scripts/hhblitsdb.pl    $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl

deinstall:
	$(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR)
	rm -f $(INSTALL_DIR)/bin/hhblits $(INSTALL_DIR)/bin/hhalign \
		$(INSTALL_DIR)/bin/hhconsensus $(INSTALL_DIR)/bin/hhfilter $(INSTALL_DIR)/bin/hhmake $(INSTALL_DIR)/bin/hhsearch
	rm -f $(INSTALL_DATA_DIR)/context_data.lib $(INSTALL_DATA_DIR)/cs219.lib $(INSTALL_DATA_DIR)/do_not_delete \
		$(INSTALL_DATA_DIR)/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.psq
	rm -f $(INSTALL_SCRIPTS_DIR)/Align.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/splitfasta.pl \
		$(INSTALL_SCRIPTS_DIR)/addss.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl \
		$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl $(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl \
		$(INSTALL_SCRIPTS_DIR)/reformat.pl $(INSTALL_SCRIPTS_DIR)/multithread.pl $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
	rm -f $(INSTALL_LIB_BIN_DIR)/cstranslate 
	rmdir $(INSTALL_LIB_BIN_DIR) || true
	rmdir $(INSTALL_DIR)/bin || true
	rmdir $(INSTALL_DATA_DIR) || true
	rmdir $(INSTALL_SCRIPTS_DIR) || true
	rmdir $(INSTALL_LIB_DIR) || true

.PHONY: clean
clean:
	cd lib/ffindex && $(MAKE) clean
	$(MAKE) -C src clean

dist/$(dist_name).tar.gz:
	make clean
	mkdir -p dist
	git archive --prefix=$(dist_name)/ -o dist/$(dist_name).tar.gz HEAD
	cd dist && tar xf $(dist_name).tar.gz
	mkdir -p dist/$(dist_name)/bin
	cd dist/$(dist_name) && rsync --exclude .git --exclude .hg -av ../../lib .
	cd dist && tar czf $(dist_name).tar.gz $(dist_name)