--- Makefile.orig	2019-05-05 03:49:17 UTC
+++ Makefile
@@ -1,11 +1,21 @@
-CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
-CPPFLAGS=	-DHAVE_KALLOC
+# Patches using ?= and adding install target were rejected by developers
+# https://github.com/lh3/minimap2/issues/388
+CFLAGS?=	-g -Wall -O2
+CFLAGS+=	-Wc++-compat #-Wextra
+CPPFLAGS+=	-DHAVE_KALLOC
 INCLUDES=
 OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
 PROG=		minimap2
 PROG_EXTRA=	sdust minimap2-lite
 LIBS=		-lm -lz -lpthread
 
+PREFIX?=	/usr/local
+DESTDIR?=	.
+MAN1DIR?=	${PREFIX}/man/man1
+MKDIR?=		mkdir
+INSTALL?=	install
+STRIP?=		strip
+
 ifeq ($(arm_neon),) # if arm_neon is not defined
 ifeq ($(sse2only),) # if sse2only is not defined
 	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
@@ -84,6 +94,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
 		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
 
 # other non-file targets
+
+install: all
+	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+	${MKDIR} -p ${DESTDIR}${MAN1DIR}
+	${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
+
+install-strip: install
+	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
 
 clean:
 		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*