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Bacon" Date: Wed, 24 Apr 2019 18:03:49 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r499895 - in head/biology: . minimap2 minimap2/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . minimap2 minimap2/files X-SVN-Commit-Revision: 499895 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: B2DB272AB9 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.97 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.97)[-0.971,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 24 Apr 2019 18:03:51 -0000 Author: jwb Date: Wed Apr 24 18:03:49 2019 New Revision: 499895 URL: https://svnweb.freebsd.org/changeset/ports/499895 Log: biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Added: head/biology/minimap2/ head/biology/minimap2/Makefile (contents, props changed) head/biology/minimap2/distinfo (contents, props changed) head/biology/minimap2/files/ head/biology/minimap2/files/patch-Makefile (contents, props changed) head/biology/minimap2/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Apr 24 18:02:45 2019 (r499894) +++ head/biology/Makefile Wed Apr 24 18:03:49 2019 (r499895) @@ -66,6 +66,7 @@ SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate + SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes Added: head/biology/minimap2/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/minimap2/Makefile Wed Apr 24 18:03:49 2019 (r499895) @@ -0,0 +1,25 @@ +# $FreeBSD$ + +PORTNAME= minimap2 +DISTVERSIONPREFIX= v +DISTVERSION= 2.16 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +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 + +USES= gmake +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +INSTALL_TARGET= install-strip +PLIST_FILES= bin/minimap2 man/man1/minimap2.1.gz + +.include Added: head/biology/minimap2/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/minimap2/distinfo Wed Apr 24 18:03:49 2019 (r499895) @@ -0,0 +1,3 @@ +TIMESTAMP = 1555901297 +SHA256 (lh3-minimap2-v2.16_GH0.tar.gz) = 9d4f1c9f1c2b29c2560b7ad53b2210dabd82161a0f88184f423534bd289433c3 +SIZE (lh3-minimap2-v2.16_GH0.tar.gz) = 221287 Added: head/biology/minimap2/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/minimap2/files/patch-Makefile Wed Apr 24 18:03:49 2019 (r499895) @@ -0,0 +1,40 @@ +--- Makefile.orig 2019-02-28 20:49:24 UTC ++++ Makefile +@@ -1,11 +1,19 @@ +-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra +-CPPFLAGS= -DHAVE_KALLOC ++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 chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o + PROG= minimap2 + PROG_EXTRA= sdust minimap2-lite + LIBS= -lm -lz -lpthread + ++PREFIX?= /usr/local ++DESTDIR?= . ++MAN1DIR?= ${PREFIX}/man/man1 ++MKDIR?= mkdir ++INSTALL?= install ++STRIP?= strip ++ + ifeq ($(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 +@@ -84,6 +92,15 @@ 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 ++ ++install: all ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${MKDIR} -p ${DESTDIR}${MAN1DIR} ++ ${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR} ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2 + + clean: + rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* Added: head/biology/minimap2/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/minimap2/pkg-descr Wed Apr 24 18:03:49 2019 (r499895) @@ -0,0 +1,18 @@ +Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA +sequences against a large reference database. Typical use cases include: + +(1) mapping PacBio or Oxford Nanopore genomic reads to the human genome + +(2) finding overlaps between long reads with error rate up to ~15% + +(3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA + readsagainst a reference genome + +(4) aligning Illumina single- or paired-end reads + +(5) assembly-to-assembly alignment + +(6) full-genome alignment between two closely related species with divergence + below ~15% + +WWW: https://github.com/lh3/minimap2