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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
-DISTVERSIONPREFIX= v
-CATEGORIES= biology
+PORTNAME= bowtie2
+PORTVERSION= 2.2.9
+DISTVERSIONPREFIX=v
+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

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