Index: biology/bowtie2/Makefile
===================================================================
--- biology/bowtie2/Makefile
+++ biology/bowtie2/Makefile
@@ -1,25 +1,28 @@
 # Created by: Jason Bacon
 # $FreeBSD$
 
-PORTNAME=		bowtie2
-PORTVERSION=		2.2.8
+PORTNAME=	bowtie2
+PORTVERSION=	2.2.9
 DISTVERSIONPREFIX=	v
-CATEGORIES=		biology
+CATEGORIES=	biology
 
 MAINTAINER=	bacon4000@gmail.com
 COMMENT=	Ultrafast, memory-efficient short read aligner
 
-LICENSE=	GPLv3
+LICENSE=	GPLv3+
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
 # May also work on other 64-bit platforms, but untested
 ONLY_FOR_ARCHS=	amd64
-USES=		gmake perl5 shebangfix
+USES=		gmake perl5 python shebangfix
 USE_PERL5=	run
-SHEBANG_FILES=	scripts/*.pl
+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} \
@@ -30,11 +33,11 @@
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${STAGEDIR}${DATADIR}/scripts
-	cd ${WRKSRC}/example && ${COPYTREE_SHARE} \
-		'index reads reference' \
-		${STAGEDIR}${EXAMPLESDIR}
-	cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \
-		\* \
-		${STAGEDIR}${DOCSDIR}
+
+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: biology/bowtie2/distinfo
===================================================================
--- biology/bowtie2/distinfo
+++ biology/bowtie2/distinfo
@@ -1,2 +1,3 @@
-SHA256 (BenLangmead-bowtie2-v2.2.8_GH0.tar.gz) = e4795f5779dfdefffcc9c341239c1fb6f7d78e15528c6094d9c580a5c0e87ac1
-SIZE (BenLangmead-bowtie2-v2.2.8_GH0.tar.gz) = 5814699
+TIMESTAMP = 1475861880
+SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee
+SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106