svn commit: r499895 - in head/biology: . minimap2 minimap2/files
Jason W. Bacon
jwb at FreeBSD.org
Wed Apr 24 18:03:51 UTC 2019
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 at 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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