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MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying transcription factor (TF) binding sites. Such sites are generated by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq (Assay for Transposase Accessible Chromatin Sequencing). MACS identifies "peaks" in the genome sequence, which are areas enriched in bound TFs or accessible chromatin.
50 lines
1.6 KiB
Makefile
50 lines
1.6 KiB
Makefile
PORTNAME= MACS3
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DISTVERSIONPREFIX= v
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DISTVERSION= 3.0.0
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CATEGORIES= biology python
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Peak caller aimed at transcription factor binding sites
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WWW= https://github.com/taoliu/MACS
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE
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BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \
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${PYNUMPY} \
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simde>0:devel/simde \
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${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
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RUN_DEPENDS= ${PYNUMPY} \
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${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
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TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
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bash:shells/bash
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USES= localbase perl5 python shebangfix
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USE_GITHUB= yes
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USE_PERL5= test
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USE_PYTHON= autoplist concurrent cython pep517
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GH_ACCOUNT= macs3-project
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GH_PROJECT= MACS
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SHEBANG_FILES= test/cmdlinetest* test/prockreport test/*.py test/pyprofile*
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.include <bsd.port.options.mk>
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.if ${OPSYS} == FreeBSD && ${OSVERSION} < 1302509
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IGNORE= does not run properly on FreeBSD 13.2 and earlier due to use of dynamically loaded libc by py-threadpoolctl. Please upgrade to a newer FreeBSD or use py-macs2 instead. See PR 276231
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.endif
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post-stage:
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${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS3/*/*.so
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# FIXME: Some tests fail due to a py-threadpoolctl issue
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# https://github.com/joblib/threadpoolctl/pull/148
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do-test: deinstall install
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@${RM} -rf ${WRKSRC}/temp
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@cd ${WRKSRC}/test && ./cmdlinetest tag
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.include <bsd.port.mk>
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