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PORTNAME= kallisto
DISTVERSIONPREFIX= v
DISTVERSION= 0.50.1
PORTEPOCH= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Quantify abundances of transcripts from RNA-Seq data
WWW= https://pachterlab.github.io/kallisto/about.html
LICENSE= BSD2CLAUSE
LICENSE_FILE= ${WRKSRC}/license.txt
ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64
ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor
LIB_DEPENDS= libhdf5.so:science/hdf5 \
libsz.so:science/libaec \
libhts.so:biology/htslib
USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags
USE_GITHUB= yes
GH_ACCOUNT= pachterlab
SUB_FILES= kallisto-test
PORTEXAMPLES= *
PLIST_FILES= bin/kallisto
EXAMPLES_PLIST_FILES= bin/kallisto-test
# hdf5 is being phased out and is no longer built in by default, but is still
# required for Sleuth (requires kallisto bootstrap estimates) and other
# downstream tools. Remove this after Sleuth et al catch up.
CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON
# WIP: Remove before committing
CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
MAKE_JOBS_UNSAFE= yes
LDFLAGS+= -lhts -lz
OPTIONS_DEFINE= EXAMPLES
post-extract:
${RM} -rf ${WRKSRC}/ext/htslib
post-install-EXAMPLES-on:
${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
.include <bsd.port.mk>
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