Index: head/biology/bowtie2/Makefile
===================================================================
--- head/biology/bowtie2/Makefile	(revision 434939)
+++ head/biology/bowtie2/Makefile	(revision 434940)
@@ -1,43 +1,45 @@
 # Created by: Jason Bacon
 # $FreeBSD$
 
 PORTNAME=	bowtie2
-PORTVERSION=	2.2.9
+PORTVERSION=	2.3.0
 DISTVERSIONPREFIX=	v
 CATEGORIES=	biology
 
 MAINTAINER=	bacon4000@gmail.com
 COMMENT=	Ultrafast, memory-efficient short read aligner
 
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS+=	libtbb.so:devel/tbb
 
 # May also work on other 64-bit platforms, but untested
 ONLY_FOR_ARCHS=	amd64
 USES=		gmake perl5 python shebangfix
 USE_PERL5=	run
 SHEBANG_FILES=	bowtie2-build bowtie2-inspect scripts/*.pl 
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	BenLangmead
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
 post-install:
 	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_PROGRAM} \
 		${WRKSRC}/bowtie2*-s \
 		${WRKSRC}/bowtie2*-l \
 		${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${STAGEDIR}${DATADIR}/scripts
 
 post-install-DOCS-on:
 	(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
 
 post-install-EXAMPLES-on:
 	(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
 
 .include <bsd.port.mk>
Index: head/biology/bowtie2/distinfo
===================================================================
--- head/biology/bowtie2/distinfo	(revision 434939)
+++ head/biology/bowtie2/distinfo	(revision 434940)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1475861880
-SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee
-SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106
+TIMESTAMP = 1487550143
+SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221
+SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016
Index: head/biology/bowtie2/files/patch-Makefile
===================================================================
--- head/biology/bowtie2/files/patch-Makefile	(revision 434939)
+++ head/biology/bowtie2/files/patch-Makefile	(revision 434940)
@@ -1,22 +1,49 @@
---- Makefile.orig	2016-02-11 17:20:57 UTC
+--- Makefile.orig	2016-12-30 15:40:06 UTC
 +++ Makefile
 @@ -21,8 +21,8 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
  #
  
 -prefix = /usr/local
 -bindir = $(prefix)/bin
 +PREFIX ?= /usr/local
 +bindir = $(PREFIX)/bin
  
  INC =
  GCC_PREFIX = $(shell dirname `which gcc`)
-@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 
+@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
+     INC += -I third_party
+ endif
+ 
++INC += -I ${LOCALBASE}/include
++
+ MM_DEF =
+ 
+ ifeq (1,$(BOWTIE_MM))
+@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
+ endif
+ 
+ PTHREAD_PKG =
+-PTHREAD_LIB =
++PTHREAD_LIB = 
+ 
+ #if we're not using TBB, then we can't use queuing locks
+ ifeq (1,$(NO_TBB))
+@@ -94,7 +96,7 @@ endif
+ 
+ #default is to use Intel TBB
+ ifneq (1,$(NO_TBB))
+-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
++	LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
+ 	override EXTRA_FLAGS += -DWITH_TBB
+ else
+ 	LIBS = $(PTHREAD_LIB)
+@@ -185,7 +187,7 @@ SSE_FLAG=-msse2
  
  DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
 -RELEASE_FLAGS  = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
 +RELEASE_FLAGS  = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops
  RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
  NOASSERT_FLAGS = -DNDEBUG
  FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
Index: head/biology/bowtie2/files/patch-aligner__result.cpp
===================================================================
--- head/biology/bowtie2/files/patch-aligner__result.cpp	(nonexistent)
+++ head/biology/bowtie2/files/patch-aligner__result.cpp	(revision 434940)
@@ -0,0 +1,13 @@
+https://github.com/BenLangmead/bowtie2/issues/81
+
+--- aligner_result.cpp.orig	2016-12-30 15:40:06 UTC
++++ aligner_result.cpp
+@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
+ 	else if(!nfilt_  ) flag = "NS";
+ 	else if(!scfilt_ ) flag = "SC";
+ 	else if(!qcfilt_ ) flag = "QC";
+-	if(flag > 0) {
++	if(*flag != '\0') {
+ 		if(!first) o.append('\t');
+ 		o.append("YF:Z:");
+ 		o.append(flag);

Property changes on: head/biology/bowtie2/files/patch-aligner__result.cpp
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property