Index: head/biology/bowtie2/Makefile
===================================================================
--- head/biology/bowtie2/Makefile
+++ head/biology/bowtie2/Makefile
@@ -1,25 +1,23 @@
-# Created by: Jason Bacon
 # $FreeBSD$
 
 PORTNAME=	bowtie2
-PORTVERSION=	2.3.0
-PORTREVISION=	2
+PORTVERSION=	2.3.3.1
 DISTVERSIONPREFIX=	v
 CATEGORIES=	biology
 
-MAINTAINER=	bacon4000@gmail.com
+MAINTAINER=	jwb@FreeBSD.org
 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
+LIB_DEPENDS=	libtbb.so:devel/tbb
+
 USES=		gmake perl5 python shebangfix
 USE_PERL5=	run
-SHEBANG_FILES=	bowtie2-build bowtie2-inspect scripts/*.pl 
+SHEBANG_FILES=	bowtie2-build bowtie2-inspect scripts/*.pl
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	BenLangmead
Index: head/biology/bowtie2/distinfo
===================================================================
--- head/biology/bowtie2/distinfo
+++ head/biology/bowtie2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1487550143
-SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221
-SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016
+TIMESTAMP = 1511991430
+SHA256 (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 8b9c0b9c595ebcddcac5feaf6acb44b2294d6deb91de107596ecad242a1a58e9
+SIZE (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 5796279
Index: head/biology/bowtie2/files/patch-Makefile
===================================================================
--- head/biology/bowtie2/files/patch-Makefile
+++ head/biology/bowtie2/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig	2016-12-30 15:40:06 UTC
+--- Makefile.orig	2017-10-05 16:45:18 UTC
 +++ Makefile
-@@ -21,8 +21,8 @@
+@@ -21,10 +21,11 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
  #
  
@@ -9,36 +9,21 @@
 +PREFIX ?= /usr/local
 +bindir = $(PREFIX)/bin
  
- INC =
+ INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include)
++INC += -I${LOCALBASE}/include
+ LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
  GCC_PREFIX = $(shell dirname `which gcc`)
-@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
-     INC += -I third_party
- endif
+ GCC_SUFFIX =
+@@ -98,7 +99,7 @@ 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
+-	LIBS += $(PTHREAD_LIB) -ltbb -ltbbmalloc$(if $(RELEASE_BUILD),,_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
+ 	LIBS += $(PTHREAD_LIB)
+@@ -189,7 +190,7 @@ SSE_FLAG=-msse2
  
  DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
Index: head/biology/bowtie2/files/patch-aligner__result.cpp
===================================================================
--- head/biology/bowtie2/files/patch-aligner__result.cpp
+++ head/biology/bowtie2/files/patch-aligner__result.cpp
@@ -1,13 +0,0 @@
-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);
Index: head/biology/bowtie2/pkg-plist
===================================================================
--- head/biology/bowtie2/pkg-plist
+++ head/biology/bowtie2/pkg-plist
@@ -34,7 +34,6 @@
 %%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png
 %%PORTDOCS%%%%DOCSDIR%%/manual.html
 %%PORTDOCS%%%%DOCSDIR%%/release.txt
-%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl
 %%PORTDOCS%%%%DOCSDIR%%/style.css
 %%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi