Description: Patch to top level Makefile
  * Make Makefile DESTDIR-aware.
  * Fix install mode of data files.
Forwarded: upstream is aware of these patches
 Upstream is Andreas Hauser <hauser@genzentrum.lmu.de>.
Author: Laszlo Kajan <lkajan@rostlab.org>
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
-# This can be overridden e.g.: make install INSTALL_DIR=...
-INSTALL_DIR?=$(PWD)
+# This can be overridden e.g.: make install PREFIX=...
+PREFIX:=/usr
 
 # Guess wether to use lib or lib64
 #libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
@@ -8,19 +8,17 @@ 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_DIR?=$(PREFIX)/$(libdir)/hhsuite
+INSTALL_SCRIPTS_DIR?=$(PREFIX)/share/hhsuite/scripts
+INSTALL_DATA_DIR?=$(PREFIX)/share/hhsuite/data
+INSTALL_BDATA_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
+all:
+	$(MAKE) -C data all
 	$(MAKE) -C src all
 
 doc:
@@ -40,35 +38,34 @@ 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
+	mkdir -p $(DESTDIR)$(PREFIX)/bin
+	install src/hhblits     $(DESTDIR)$(PREFIX)/bin/hhblits
+	install src/hhalign     $(DESTDIR)$(PREFIX)/bin/hhalign
+	install src/hhconsensus $(DESTDIR)$(PREFIX)/bin/hhconsensus
+	install src/hhfilter    $(DESTDIR)$(PREFIX)/bin/hhfilter
+	install src/hhmake      $(DESTDIR)$(PREFIX)/bin/hhmake
+	install src/hhsearch    $(DESTDIR)$(PREFIX)/bin/hhsearch
+	mkdir -p $(DESTDIR)$(INSTALL_LIB_DIR)
+	mkdir -p $(DESTDIR)$(INSTALL_LIB_BIN_DIR)
+	install src/cstranslate $(DESTDIR)$(INSTALL_LIB_BIN_DIR)/cstranslate
+	mkdir -p $(DESTDIR)$(INSTALL_DATA_DIR) $(DESTDIR)$(INSTALL_BDATA_DIR)
+	install --mode=0644 data/context_data.lib $(DESTDIR)$(INSTALL_DATA_DIR)/context_data.lib
+	install --mode=0644 data/cs219.lib        $(DESTDIR)$(INSTALL_DATA_DIR)/cs219.lib
+	install --mode=0644 data/do_not_delete    $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete
+	install --mode=0644 data/do_not_delete.phr $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.phr
+	install --mode=0644 data/do_not_delete.pin $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.pin
+	install --mode=0644 data/do_not_delete.psq $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.psq
+	mkdir -p $(DESTDIR)$(INSTALL_SCRIPTS_DIR)
+	install --mode=0644 scripts/Align.pm        $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/Align.pm
+	install --mode=0644 scripts/HHPaths.pm      $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/HHPaths.pm
+	install scripts/addss.pl        $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/addss.pl
+	install scripts/create_profile_from_hhm.pl   $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl
+	install scripts/create_profile_from_hmmer.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl
+	install scripts/hhmakemodel.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl
+	install scripts/reformat.pl    $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/reformat.pl
+	install scripts/splitfasta.pl  $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/splitfasta.pl
+	install scripts/multithread.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/multithread.pl
+	install scripts/hhblitsdb.pl   $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
 
 deinstall:
 	$(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR)
@@ -89,9 +86,11 @@ deinstall:
 
 .PHONY: clean
 clean:
-	cd lib/ffindex && $(MAKE) clean
 	$(MAKE) -C src clean
 
+.PHONY: distclean
+distclean: clean
+
 dist/$(dist_name).tar.gz:
 	make clean
 	mkdir -p dist
