Index: head/biology/bowtie/Makefile
===================================================================
--- head/biology/bowtie/Makefile	(revision 483952)
+++ head/biology/bowtie/Makefile	(revision 483953)
@@ -1,49 +1,48 @@
 # $FreeBSD$
 
 PORTNAME=		bowtie
+PORTVERSION=		1.1.2
+PORTREVISION=	6
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.1.2
-PORTREVISION=		7
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Ultrafast, memory-efficient short read aligner
 
 LICENSE=	ART10
 
 # May also work on other 64-bit platforms, but untested
 ONLY_FOR_ARCHS=	amd64
-
-USES=		gmake perl5 python:run shebangfix
 # FIXME: bowtie-align intermittently dumps core when compiled with clang
 # GCC 4.2 does not provide good performance
 USE_GCC=	yes
+USES=		gmake perl5 python:run shebangfix
 USE_PERL5=	run
-
-SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build bowtie-inspect
+SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build \
+		bowtie-inspect
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	BenLangmead
 
 OPTIONS_DEFINE=	DOCS
 
 post-install:
 	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/bowtie \
 		${WRKSRC}/bowtie-build \
 		${WRKSRC}/bowtie-inspect \
 		${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${STAGEDIR}${DATADIR}/scripts
 	cd ${WRKSRC} && ${COPYTREE_SHARE} \
 		'genomes indexes reads' \
 		${STAGEDIR}${DATADIR}
 	cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \
 		\* \
 		${STAGEDIR}${DOCSDIR}
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*-[sl]
 
 .include <bsd.port.mk>
Index: head/biology/bowtie/files/patch-ebwt.h
===================================================================
--- head/biology/bowtie/files/patch-ebwt.h	(revision 483952)
+++ head/biology/bowtie/files/patch-ebwt.h	(nonexistent)
@@ -1,11 +0,0 @@
---- ebwt.h.orig	2018-11-03 20:51:56 UTC
-+++ ebwt.h
-@@ -860,7 +860,7 @@ public:
- 	TIndexOffU*   ftab() const         { return _ftab; }
- 	TIndexOffU*   eftab() const        { return _eftab; }
- 	TIndexOffU*   offs() const         { return _offs; }
--	uint32_t*   isa() const          { return _isa; } /* check */
-+	uint32_t*   isa() const          { return (uint32_t)_isa; } /* check */
- 	TIndexOffU*   plen() const         { return _plen; }
- 	TIndexOffU*   rstarts() const      { return _rstarts; }
- 	uint8_t*    ebwt() const         { return _ebwt; }

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