5 files changed, 87 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index b1c2b00e8bad..4ceee59bafa8 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -66,6 +66,7 @@
     SUBDIR += mafft
     SUBDIR += mapm3
     SUBDIR += migrate
+    SUBDIR += minimap2
     SUBDIR += molden
     SUBDIR += mopac
     SUBDIR += mrbayes
diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
new file mode 100644
index 000000000000..528872dd26b8
--- /dev/null
+++ b/biology/minimap2/Makefile
@@ -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>
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
new file mode 100644
index 000000000000..4167b37be746
--- /dev/null
+++ b/biology/minimap2/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1555901297
+SHA256 (lh3-minimap2-v2.16_GH0.tar.gz) = 9d4f1c9f1c2b29c2560b7ad53b2210dabd82161a0f88184f423534bd289433c3
+SIZE (lh3-minimap2-v2.16_GH0.tar.gz) = 221287
diff --git a/biology/minimap2/files/patch-Makefile b/biology/minimap2/files/patch-Makefile
new file mode 100644
index 000000000000..19bf99b1325d
--- /dev/null
+++ b/biology/minimap2/files/patch-Makefile
@@ -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*
diff --git a/biology/minimap2/pkg-descr b/biology/minimap2/pkg-descr
new file mode 100644
index 000000000000..a9d86305f0f5
--- /dev/null
+++ b/biology/minimap2/pkg-descr
@@ -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