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1.2
date	2025.03.06.01.19.02;	author bacon;	state Exp;
branches;
next	1.1;
commitid	ttX4UUbgIuqcEWLF;

1.1
date	2024.10.11.22.44.39;	author bacon;	state Exp;
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commitid	rEs6evOsSGe1sitF;


desc
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1.2
log
@Multiple packages: OWNER -> MAINTAINER
@
text
@# $NetBSD: Makefile,v 1.1 2024/10/11 22:44:39 bacon Exp $

DISTNAME=	bio-mocha-1.20
CATEGORIES=	biology
# Can't get ${MASTER_SITE_GITHUB:=samtools/} to work with additional distfile
MASTER_SITES=	https://software.broadinstitute.org/software/mocha/
MASTER_SITES+=	https://github.com/samtools/bcftools/releases/download/${GH_TAG}/
DISTFILES+=	bio-mocha_1.20-20240505.tar.gz
DISTFILES+=	bcftools-1.21.tar.bz2
GH_TAG=		1.21

MAINTAINER=	bacon@@NetBSD.org
HOMEPAGE=	https://software.broadinstitute.org/software/mocha/
COMMENT=	Bcftools plugin for mosaic chromosomal alteration analysis
LICENSE=	mit

REPLACE_INTERPRETER+=	R
REPLACE.R.old=		/usr/bin/env Rscript
REPLACE.R.new=		${PREFIX}/bin/Rscript
REPLACE_FILES.R=	MoCha/*.R

SUBST_CLASSES+=		version
SUBST_STAGE.version=	pre-configure
SUBST_SED.version=	-e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
SUBST_FILES.version=	configure.ac

DEPENDS=	bash>=0:../../shells/bash
DEPENDS+=	bcftools>=1.16:../../biology/bcftools

USE_TOOLS+=	autoconf automake autoreconf bash gmake perl pax
GNU_CONFIGURE=	yes
REPLACE_PERL=	misc/* test/test.pl

WRKSRC=		${WRKDIR}/bcftools-${GH_TAG}

DATADIR=		${PREFIX}/share/bio-mocha
# FIXME: Why is share/bio-mocha only required on macOS?
INSTALLATION_DIRS=	libexec/bcftools share/bio-mocha

post-extract:
	${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
	${MKDIR} ${WRKSRC}/MoCha
	${CP} ${WRKDIR}/*.R ${WRKSRC}/MoCha

pre-configure:
	cd ${WRKSRC} && autoreconf -if

# One .so for each .c in the mocha distfile
do-install:
	${INSTALL_PROGRAM} ${WRKSRC}/plugins/extendFMT.so \
		${DESTDIR}${PREFIX}/libexec/bcftools
	${INSTALL_PROGRAM} ${WRKSRC}/plugins/mocha.so \
		${DESTDIR}${PREFIX}/libexec/bcftools
	${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \
		${DESTDIR}${PREFIX}/libexec/bcftools
	(cd ${WRKSRC}/MoCha && pax -rw . ${DESTDIR}${DATADIR})

.include "../../devel/zlib/buildlink3.mk"
.include "../../math/gsl/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../biology/htslib/buildlink3.mk"
.include "../../math/R/buildlink3.mk"
# Required for Linux, even though inherited from htslib
.include "../../archivers/bzip2/buildlink3.mk"
.include "../../archivers/xz/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
@


1.1
log
@biology/bio-mocha: Bcftools plugin for mCA analysis

MoChA is a bcftools plugin released under the MIT license for mosaic
chromosomal alteration detection and analysis from DNA microarray or
whole genome sequence data. It can be used both with Illumina and
Affymetrix data. It can also be used for detection of germline copy
number variants. Data can be prepared in usable file formats using the
gtc2vcf plugin.
@
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OWNER=		bacon@@NetBSD.org
@