# $NetBSD$
#
###########################################################
#                  Generated by fbsd2pkg                  #
#              Fri Nov  3 16:02:27 CDT 2017               #
###########################################################

DISTNAME=	fastqc_v${PORTVERSION}
PKGNAME=	fastqc-${PORTVERSION}
CATEGORIES=	biology
MASTER_SITES=	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
EXTRACT_SUFX=	.zip

MAINTAINER=	bacon@NetBSD.org
HOMEPAGE=	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
COMMENT=	Quality control tool for high throughput sequence data
# Check this
LICENSE=	gnu-gpl-v3

SUBST_CLASSES+=		javapath
SUBST_STAGE.javapath=	post-patch
SUBST_SED.javapath+=	-e 's|$$RealBin$$delimiter|${DATADIR}$$delimiter${JAVAJARDIR}/fastqc$$delimiter|g'
SUBST_SED.javapath+=	-e 's|$$RealBin/|${JAVAJARDIR}/fastqc/|g'
SUBST_FILES.javapath+=	${WRKSRC}/fastqc

USE_TOOLS+=	perl:run pax
REPLACE_PERL=	fastqc
NO_BUILD=	yes

WRKSRC=		${WRKDIR}/FastQC

# Normal extract is corrupting org/apache/commons/math3/distribution/IntegerDistribution.class due to a bug in archivers/unzip -a
EXTRACT_OPTS_ZIP=	-qo

PORTVERSION=	0.11.5
DATADIR=	${PREFIX}/share/fastqc
DOCSDIR=	${PREFIX}/share/doc/fastqc
USE_JAVA=	yes
JAVAJARDIR=	${PREFIX}/share/java/classes

INSTALLATION_DIRS=	bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}/fastqc

do-install:
	${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}/fastqc
	${INSTALL_SCRIPT} ${WRKSRC}/fastqc \
		${DESTDIR}${PREFIX}/bin
	cd ${WRKSRC} && pax -rw Configuration \
		${DESTDIR}${DATADIR}
	cd ${WRKSRC} && pax -rw Templates \
		${DESTDIR}${DATADIR}
	cd ${WRKSRC} && pax -rw net \
		${DESTDIR}${JAVAJARDIR}/fastqc
	cd ${WRKSRC} && pax -rw org \
		${DESTDIR}${JAVAJARDIR}/fastqc
	cd ${WRKSRC} && pax -rw uk \
		${DESTDIR}${JAVAJARDIR}/fastqc
	cd ${WRKSRC} && pax -rw 'Help' \
		${DESTDIR}${DOCSDIR}

.include "../../mk/bsd.pkg.mk"
