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biology/minimap2: Update to 2.20

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Add "extra" binaries to install

Changes:    https://github.com/lh3/minimap2/releases/tag/v2.20
This commit is contained in:
Jason W. Bacon 2021-05-29 16:06:34 -05:00
parent 33999d3894
commit da0bb00a74
3 changed files with 30 additions and 14 deletions
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11
biology/minimap2/Makefile
View File

@ -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>

6
biology/minimap2/distinfo
View File

@ -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

27
biology/minimap2/files/patch-Makefile
View File

@ -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*