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PORTNAME= haplohseq
DISTVERSION= 0.1.2
PORTREVISION= 5
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Identify regions of allelic imbalance
WWW= https://sites.google.com/site/integrativecancergenomics/software/haplohseq
LICENSE= MIT
LIB_DEPENDS= libboost_system.so:devel/boost-libs
RUN_DEPENDS= R-cran-optparse>0:devel/R-cran-optparse
USES= compiler:c++11-lang gmake localbase:ldflags python:3.6+
USE_GITHUB= yes
GH_ACCOUNT= outpaddling
OPTIONS_DEFINE= EXAMPLES
MAKEFILE= makefile
LDFLAGS+= -lpthread
MAKE_ENV= STRIP=${STRIP}
SUB_FILES= haplohseq-example
pre-configure:
@${REINPLACE_CMD} \
-e 's|/bin/bash|/bin/sh|' \
-e 's|python|mkdir example_output; ${PYTHON_CMD}|' \
-e 's|\.\./haplohseq|haplohseq|' \
${WRKSRC}/example/example_run.sh
post-install-EXAMPLES-on:
${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${STAGEDIR}${PREFIX}/bin
(cd ${WRKSRC} && ${RM} example/*.orig scripts/*.orig && ${COPYTREE_SHARE} "example ldmap scripts" ${STAGEDIR}${EXAMPLESDIR})
do-test:
@(cd ${WRKSRC}/build/test && ${FILESDIR}/run-tests)
.include <bsd.port.mk>
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