git: da0bb00a7464 - main - biology/minimap2: Update to 2.20

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=da0bb00a74646f1a22eed576fb041c0d04a03a19

commit da0bb00a74646f1a22eed576fb041c0d04a03a19
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-05-29 21:06:34 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-05-29 21:06:34 +0000

    biology/minimap2: Update to 2.20
    
    Add "extra" binaries to install
    
    Changes:    https://github.com/lh3/minimap2/releases/tag/v2.20
---
 biology/minimap2/Makefile             | 11 +++++++----
 biology/minimap2/distinfo             |  6 +++---
 biology/minimap2/files/patch-Makefile | 27 ++++++++++++++++++++-------
 3 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index d99da2bcc4b5..2f3f34aeef46 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.18
+DISTVERSION=		2.20
 CATEGORIES=		biology
 
 MAINTAINER=	jwb at FreeBSD.org
@@ -9,15 +9,18 @@ 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
+ONLY_FOR_ARCHS_REASON=	Hard-coded SSE instructions
 
 USES=		gmake
 USE_GITHUB=	yes
+
 GH_ACCOUNT=	lh3
 
+MAKE_ARGS+=	CFLAGS+=-Wextra
+ALL_TARGET=	extra
 INSTALL_TARGET=	install-strip
-PLIST_FILES=	bin/minimap2 man/man1/minimap2.1.gz
+
+PLIST_FILES=	bin/minimap2 bin/minimap2-lite bin/sdust man/man1/minimap2.1.gz
 
 .include <bsd.port.mk>
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
index 69632d44a87f..94d841b72134 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1618167822
-SHA256 (lh3-minimap2-v2.18_GH0.tar.gz) = efe75148342decd67e16f6a9ae14918ab9e1d67cadcfab5698b847f5b66f55e3
-SIZE (lh3-minimap2-v2.18_GH0.tar.gz) = 231187
+TIMESTAMP = 1622319613
+SHA256 (lh3-minimap2-v2.20_GH0.tar.gz) = 8153a0dda3c16da13d70b893ab7ea93366136f147407aab994bffe5eaa93e897
+SIZE (lh3-minimap2-v2.20_GH0.tar.gz) = 239973
diff --git a/biology/minimap2/files/patch-Makefile b/biology/minimap2/files/patch-Makefile
index 19bf99b1325d..1de7e1c5e6ee 100644
--- a/biology/minimap2/files/patch-Makefile
+++ b/biology/minimap2/files/patch-Makefile
@@ -1,19 +1,19 @@
---- Makefile.orig	2019-02-28 20:49:24 UTC
+--- Makefile.orig	2021-05-27 19:26:04 UTC
 +++ Makefile
-@@ -1,11 +1,19 @@
+@@ -1,5 +1,6 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 -CPPFLAGS=	-DHAVE_KALLOC
 +CFLAGS?=	-g -Wall -O2
 +CFLAGS+=	-Wc++-compat #-Wextra
-+CPPFLAGS+=	-DHAVE_KALLOC
++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
+ OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
+ 			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
+@@ -8,6 +9,12 @@ PROG=		minimap2
  PROG_EXTRA=	sdust minimap2-lite
  LIBS=		-lm -lz -lpthread
  
 +PREFIX?=	/usr/local
-+DESTDIR?=	.
 +MAN1DIR?=	${PREFIX}/man/man1
 +MKDIR?=		mkdir
 +INSTALL?=	install
@@ -22,7 +22,16 @@
  ifeq ($(arm_neon),) # if arm_neon is not defined
  ifeq ($(sse2only),) # if sse2only is not defined
  	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
-@@ -84,6 +92,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+@@ -34,7 +41,7 @@ ifneq ($(tsan),)
+ 	LIBS+=-fsanitize=thread
+ endif
+ 
+-.PHONY:all extra clean depend
++.PHONY:all extra install clean depend
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+@@ -96,6 +103,19 @@ 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
@@ -31,10 +40,14 @@
 +	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
 +	${MKDIR} -p ${DESTDIR}${MAN1DIR}
 +	${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin
 +	${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
 +
 +install-strip: install
 +	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
++	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
++	${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
  
  clean:
  		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*