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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-22 14:15:06 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-22 14:15:06 +0000 |
| commit | 205fcac2210ba735dde3e037616661ab16cd5e66 (patch) | |
| tree | 405a4bb03d58e31b0ca0db96cc3728e53d5ba864 | |
| parent | c5efaea23b875a30e9a7652734d2c992d44f9fbc (diff) | |
| download | ports-205fcac2210ba735dde3e037616661ab16cd5e66.tar.gz ports-205fcac2210ba735dde3e037616661ab16cd5e66.zip | |
biology/minimap2: Update to 2.22
Changelog: https://github.com/lh3/minimap2/releases/tag/v2.22
Reported by: portscout
| -rw-r--r-- | biology/minimap2/Makefile | 4 | ||||
| -rw-r--r-- | biology/minimap2/distinfo | 6 | ||||
| -rw-r--r-- | 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@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 |