Index: head/biology/minimap2/Makefile
===================================================================
--- head/biology/minimap2/Makefile	(revision 500859)
+++ head/biology/minimap2/Makefile	(revision 500860)
@@ -1,25 +1,25 @@
 # $FreeBSD$
 
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.16
+DISTVERSION=		2.17
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Pairwise aligner for genomic and spliced nucleotide sequences
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 # Depends on hard-coded SSE instructions
 # There appears to be some support for AARCH64 as well
 ONLY_FOR_ARCHS=	amd64 i386
 
 USES=		gmake
 USE_GITHUB=	yes
 GH_ACCOUNT=	lh3
 
 INSTALL_TARGET=	install-strip
 PLIST_FILES=	bin/minimap2 man/man1/minimap2.1.gz
 
 .include <bsd.port.mk>
Index: head/biology/minimap2/distinfo
===================================================================
--- head/biology/minimap2/distinfo	(revision 500859)
+++ head/biology/minimap2/distinfo	(revision 500860)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1555901297
-SHA256 (lh3-minimap2-v2.16_GH0.tar.gz) = 9d4f1c9f1c2b29c2560b7ad53b2210dabd82161a0f88184f423534bd289433c3
-SIZE (lh3-minimap2-v2.16_GH0.tar.gz) = 221287
+TIMESTAMP = 1557067380
+SHA256 (lh3-minimap2-v2.17_GH0.tar.gz) = 0a3eaa3ef3d9f9e41f48199cc4aac0508366ac644fc3e8fe05e3463acd23d20b
+SIZE (lh3-minimap2-v2.17_GH0.tar.gz) = 224006

Property changes on: head/biology/minimap2/distinfo
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property
Index: head/biology/minimap2/files/patch-Makefile
===================================================================
--- head/biology/minimap2/files/patch-Makefile	(revision 500859)
+++ head/biology/minimap2/files/patch-Makefile	(revision 500860)
@@ -1,40 +1,42 @@
---- Makefile.orig	2019-02-28 20:49:24 UTC
+--- Makefile.orig	2019-05-05 03:49:17 UTC
 +++ Makefile
-@@ -1,11 +1,19 @@
+@@ -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 +92,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+@@ -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*

Property changes on: head/biology/minimap2/files/patch-Makefile
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property