git: 205fcac2210b - main - biology/minimap2: Update to 2.22

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=205fcac2210ba735dde3e037616661ab16cd5e66

commit 205fcac2210ba735dde3e037616661ab16cd5e66
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-08-22 14:15:06 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-08-22 14:15:06 +0000

    biology/minimap2: Update to 2.22
    
    Changelog: https://github.com/lh3/minimap2/releases/tag/v2.22
    
    Reported by:    portscout
---
 biology/minimap2/Makefile             |  4 +---
 biology/minimap2/distinfo             |  6 +++---
 biology/minimap2/files/patch-Makefile | 16 ++++++++++++----
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index 2f3f34aeef46..dd5213d9851f 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.20
+DISTVERSION=		2.22
 CATEGORIES=		biology
 
 MAINTAINER=	jwb at FreeBSD.org
@@ -21,6 +21,4 @@ MAKE_ARGS+=	CFLAGS+=-Wextra
 ALL_TARGET=	extra
 INSTALL_TARGET=	install-strip
 
-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 94d841b72134..e52728d52312 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1622319613
-SHA256 (lh3-minimap2-v2.20_GH0.tar.gz) = 8153a0dda3c16da13d70b893ab7ea93366136f147407aab994bffe5eaa93e897
-SIZE (lh3-minimap2-v2.20_GH0.tar.gz) = 239973
+TIMESTAMP = 1629640993
+SHA256 (lh3-minimap2-v2.22_GH0.tar.gz) = b625a7580d9b5996f2553ee90ffcec84870bd9b88c009c9d71e8c1c648c53ed6
+SIZE (lh3-minimap2-v2.22_GH0.tar.gz) = 251821
diff --git a/biology/minimap2/files/patch-Makefile b/biology/minimap2/files/patch-Makefile
index 1de7e1c5e6ee..79c9c3617b38 100644
--- a/biology/minimap2/files/patch-Makefile
+++ b/biology/minimap2/files/patch-Makefile
@@ -1,28 +1,34 @@
 --- Makefile.orig	2021-05-27 19:26:04 UTC
 +++ Makefile
-@@ -1,5 +1,6 @@
+@@ -1,5 +1,9 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 -CPPFLAGS=	-DHAVE_KALLOC
++
++# Makefile patches rejected by upstream
++
 +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 \
  			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
-@@ -8,6 +9,12 @@ PROG=		minimap2
+@@ -8,6 +12,15 @@ PROG=		minimap2
  PROG_EXTRA=	sdust minimap2-lite
  LIBS=		-lm -lz -lpthread
  
 +PREFIX?=	/usr/local
 +MAN1DIR?=	${PREFIX}/man/man1
++DATADIR?=	${PREFIX}/share/minimap2
++
 +MKDIR?=		mkdir
++CP?=		cp
 +INSTALL?=	install
 +STRIP?=		strip
 +
  ifeq ($(arm_neon),) # if arm_neon is not defined
  ifeq ($(sse2only),) # if sse2only is not defined
  	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
-@@ -34,7 +41,7 @@ ifneq ($(tsan),)
+@@ -34,7 +47,7 @@ ifneq ($(tsan),)
  	LIBS+=-fsanitize=thread
  endif
  
@@ -31,7 +37,7 @@
  .SUFFIXES:.c .o
  
  .c.o:
-@@ -96,6 +103,19 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+@@ -96,6 +109,21 @@ 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
@@ -39,10 +45,12 @@
 +install: all
 +	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
 +	${MKDIR} -p ${DESTDIR}${MAN1DIR}
++	${MKDIR} -p ${DESTDIR}${DATADIR}
 +	${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}
++	${CP} -R test ${DESTDIR}${DATADIR}
 +
 +install-strip: install
 +	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2