--- core/Makefile.orig	2015-11-26 01:42:39 UTC
+++ core/Makefile
@@ -1,8 +1,7 @@
-PREFIX = /usr/local
-LIBDIR = $(PREFIX)/libexec/mafft
-BINDIR = $(PREFIX)/bin
-MANDIR = $(PREFIX)/share/man/man1
-DESTDIR = 
+prefix = ${STAGEDIR}${PREFIX}
+LIBDIR = $(prefix)/libexec/mafft
+BINDIR = $(prefix)/bin
+MANDIR = $(prefix)/share/man/man1
 
 #MNO_CYGWIN = -mno-cygwin
 
@@ -10,29 +9,17 @@ ENABLE_MULTITHREAD = -Denablemultithread
 # Comment out the above line if your compiler 
 # does not support TLS (thread-local strage).
 
-CC = gcc
-CFLAGS = -O3
-#CFLAGS = -O3 -fPIC
-# add -fPIC when building .so files
-
-#CC = icc
-#CFLAGS = -fast
-# if you have icc, use this.
-
-#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
-#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3  -fprofile-arcs -ftest-coverage 
-#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind
-
-
-MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
+MYCFLAGS = $(ENABLE_MULTITHREAD) $(CFLAGS)
 
 ifdef ENABLE_MULTITHREAD
-LIBS = -lm  -lpthread
+LIBS = -lm  -pthread
 else
 LIBS = -lm
 endif
 
-INSTALL = install
+LNFILES = linsi ginsi fftns fftnsi nwns nwnsi einsi \
+	mafft-linsi mafft-ginsi mafft-fftns mafft-fftnsi mafft-nwns \
+	mafft-nwnsi mafft-einsi mafft-xinsi mafft-qinsi
 
 PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
 		pair2hat3s multi2hat3s pairash addsingle \
@@ -131,12 +118,6 @@ MANPAGES = mafft.1 mafft-homologs.1
 
 
 all : $(PERLPROGS) $(PROGS) $(SCRIPTS)
-	cp $(SCRIPTS) ../scripts
-	chmod 755 ../scripts/*
-	cp $(PERLPROGS) $(PROGS) ../binaries
-	chmod 755 ../binaries/*
-	cp $(MANPAGES) ../binaries
-	@echo done.
 
 sos : $(SOS)
 dylibs : $(DYLIBS)
@@ -524,31 +505,13 @@ clean :
 #	rm -f ../binaries/* ../scripts/*
 
 install : all
-	mkdir -p $(DESTDIR)$(LIBDIR)
-	chmod 755 $(DESTDIR)$(LIBDIR)
-	mkdir -p $(DESTDIR)$(BINDIR)
-	chmod 755 $(DESTDIR)$(BINDIR)
-	chmod 755 $(SCRIPTS)
-	$(INSTALL) $(SCRIPTS)  $(DESTDIR)$(BINDIR)
-	chmod 755 $(PROGS) ||:     # in MinGW, it's ok if this fails
-	$(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR)
-	$(INSTALL) $(PERLPROGS) $(DESTDIR)$(LIBDIR)
-	$(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(LIBDIR)
+	$(MKDIR) $(DESTDIR)$(LIBDIR) $(DESTDIR)$(BINDIR) $(DESTDIR)$(MANDIR)
+	$(INSTALL_SCRIPT) $(SCRIPTS)  $(DESTDIR)$(BINDIR)
+	$(INSTALL_PROGRAM) $(PROGS) $(DESTDIR)$(LIBDIR)
+	$(INSTALL_SCRIPT) $(PERLPROGS) $(DESTDIR)$(LIBDIR)
+	$(INSTALL_DATA) $(MANPAGES) $(DESTDIR)$(MANDIR)
 
-	( cd $(DESTDIR)$(BINDIR); \
-rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
-rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \
-ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
-ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
-ln -s mafft einsi; \
-ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
-ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
-ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
-rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \
-rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . )
+	$(foreach f,$(LNFILES),$(LN) -s mafft $(DESTDIR)$(BINDIR)/$(f);)
 
-	mkdir -p $(DESTDIR)$(MANDIR)
-	chmod 755 $(DESTDIR)$(MANDIR)
-	$(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(MANDIR)
-# remove incorrectly installed manpages by previous versions
-#	rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1 
+	$(LN) -s ../libexec/mafft/mafft-profile $(DESTDIR)$(BINDIR)/mafft-profile
+	$(LN) -s ../libexec/mafft/mafft-distance $(DESTDIR)$(BINDIR)/mafft-distance