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PORTNAME= bowtie2
DISTVERSIONPREFIX= v
DISTVERSION= 2.4.4
CATEGORIES= biology perl5 python
MAINTAINER= jwb@FreeBSD.org
COMMENT= Ultrafast, memory-efficient short read aligner
LICENSE= GPLv3+
LICENSE_FILE= ${WRKSRC}/LICENSE
# Requires a 64-bit processor and depends on hard-coded asm instructions
ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le
RUN_DEPENDS= bash:shells/bash
USES= gmake localbase:ldflags perl5 python shebangfix
USE_PERL5= run
USE_GITHUB= yes
SHEBANG_FILES= bowtie2 bowtie2-build bowtie2-inspect \
scripts/bowtie2-hbb.sh scripts/*.pl
GH_ACCOUNT= BenLangmead
GH_TUPLE= simd-everywhere:simde-no-tests:f6a0b3b:simde
OPTIONS_DEFINE= DOCS EXAMPLES
SUB_FILES= bowtie2-test
.include <bsd.port.options.mk>
.if ${ARCH} != amd64
post-extract:
(cd ${WRKSRC_simde}; \
${COPYTREE_SHARE} . ${WRKSRC}/third_party/simde/)
MAKE_ENV= POPCNT_CAPABILITY=0
.endif
pre-configure:
@${REINPLACE_CMD} \
-e 's|^RELEASE_FLAGS|# RELEASE_FLAGS|' \
-e 's|tbbmalloc_proxy|tbbmalloc|' \
${WRKSRC}/Makefile
post-install:
@${MKDIR} ${STAGEDIR}${DATADIR}/scripts
${INSTALL_PROGRAM} \
${WRKSRC}/bowtie2*-s \
${WRKSRC}/bowtie2*-l \
${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} \
${WRKSRC}/scripts/*.sh \
${WRKSRC}/scripts/*.pl \
${STAGEDIR}${DATADIR}/scripts
${INSTALL_SCRIPT} ${WRKDIR}/bowtie2-test ${STAGEDIR}${PREFIX}/bin
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>
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