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Date:      Wed, 24 Apr 2019 18:03:49 +0000 (UTC)
From:      "Jason W. Bacon" <jwb@FreeBSD.org>
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
Message-ID:  <201904241803.x3OI3nRT097057@repo.freebsd.org>

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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 <bsd.port.mk>

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



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