Commit 08256be5 authored by Jason W. Bacon's avatar Jason W. Bacon
Browse files

biology/py-macs2: Remove 

MACS2 is dead upstream, with no plans to make it compatible with
cython 3.x or other newer dependencies.  Though the port was
set to expire in another month, I'm removing it now to stop wasting
package building resources.  It has not been buildable for some time.
parent d133edcc

biology/Makefile

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@@ -183,7 +183,6 @@ 
    SUBDIR += py-libnuml

    SUBDIR += py-libsedml

    SUBDIR += py-loompy

    SUBDIR += py-macs2

    SUBDIR += py-macs3

    SUBDIR += py-mrcfile

    SUBDIR += py-multiqc

biology/py-macs2/Makefile

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PORTNAME=		macs2

DISTVERSIONPREFIX=	v

DISTVERSION=		2.2.9.1

PORTREVISION=	3

CATEGORIES=		biology python

PKGNAMEPREFIX=		${PYTHON_PKGNAMEPREFIX}



MAINTAINER=	jwb@FreeBSD.org

COMMENT=	Identify transcription factor binding sites

WWW=		https://github.com/taoliu/MACS



LICENSE=	BSD3CLAUSE

LICENSE_FILE=	${WRKSRC}/LICENSE



DEPRECATED=	Depends on expired lang/cython0

EXPIRATION_DATE=2026-09-15



BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR}

RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \

		${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR}

TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \

		bash:shells/bash



USES=		python shebangfix

USE_GITHUB=	yes

USE_PYTHON=	autoplist concurrent cython0 distutils



GH_ACCOUNT=	taoliu

GH_PROJECT=	MACS

SHEBANG_FILES=	test/cmdlinetest_update test/cmdlinetest test/prockreport



post-stage:

	${STRIP_CMD} \

		${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*.so \

		${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*/*.so



do-test: install

	@cd ${WRKSRC}/test && ./cmdlinetest tag



.include <bsd.port.mk>

biology/py-macs2/distinfo

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TIMESTAMP = 1691269587

SHA256 (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 8e461dde82288280fe708cd4f5fec986fbf2da67b344f4dea5693af849549163

SIZE (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 133109075

biology/py-macs2/pkg-descr

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MACS is a tool for chromatin immunoprecipitation (ChIP) sequence analysis.

MACS empirically models the length of the sequenced ChIP fragments, which

tend to be shorter than sonication or library construction size estimates,

and uses it to improve the spatial resolution of predicted binding sites.