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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

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