diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-05-29 21:06:34 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-05-29 21:06:34 +0000 |
| commit | da0bb00a74646f1a22eed576fb041c0d04a03a19 (patch) | |
| tree | b754960d70430b05fb937fa87981a660474789f4 /biology/minimap2 | |
| parent | 33999d389428156e954e46cef35186018e6a0e07 (diff) | |
| download | ports-da0bb00a74646f1a22eed576fb041c0d04a03a19.tar.gz ports-da0bb00a74646f1a22eed576fb041c0d04a03a19.zip | |
biology/minimap2: Update to 2.20
Add "extra" binaries to install
Changes: https://github.com/lh3/minimap2/releases/tag/v2.20
Diffstat (limited to 'biology/minimap2')
| -rw-r--r-- | biology/minimap2/Makefile | 11 | ||||
| -rw-r--r-- | biology/minimap2/distinfo | 6 | ||||
| -rw-r--r-- | 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@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* |