# Created by: Johann Visagie <johann@egenetics.com>
# $FreeBSD$

PORTNAME=	BioPerl
PORTVERSION=	1.007002
CATEGORIES=	biology perl5
MASTER_SITES=	CPAN
MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
PKGNAMEPREFIX=	p5-

MAINTAINER=	perl@FreeBSD.org
COMMENT=	Collection of Perl modules for bioinformatics

LICENSE=	ART10 GPLv1+
LICENSE_COMB=	dual

BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
		p5-Array-Compare>=0:misc/p5-Array-Compare \
		p5-CGI>=0:www/p5-CGI \
		p5-Clone>=0:devel/p5-Clone \
		p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \
		p5-DBD-mysql>=0:databases/p5-DBD-mysql \
		p5-DBI>=0:databases/p5-DBI \
		p5-Data-Stag>=0.11:devel/p5-Data-Stag \
		p5-Error>=0:lang/p5-Error \
		p5-GD>=0:graphics/p5-GD \
		p5-Graph>=0.50:math/p5-Graph \
		p5-GraphViz>=0:graphics/p5-GraphViz \
		p5-HTML-Parser>=3:www/p5-HTML-Parser \
		p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \
		p5-HTTP-Message>=0:www/p5-HTTP-Message \
		p5-IO-String>=0:devel/p5-IO-String \
		p5-IO-stringy>=0:devel/p5-IO-stringy \
		p5-Inline-C>=0.67:devel/p5-Inline-C \
		p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
		p5-PostScript>=0:print/p5-PostScript \
		p5-SVG>=2.26:textproc/p5-SVG \
		p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \
		p5-Set-Scalar>=0:devel/p5-Set-Scalar \
		p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \
		p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \
		p5-XML-DOM>=0:textproc/p5-XML-DOM \
		p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \
		p5-XML-LibXML>=0:textproc/p5-XML-LibXML \
		p5-XML-Parser>=0:textproc/p5-XML-Parser \
		p5-XML-SAX>=0.15:textproc/p5-XML-SAX \
		p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \
		p5-XML-Simple>=0:textproc/p5-XML-Simple \
		p5-XML-Twig>=0:textproc/p5-XML-Twig \
		p5-XML-Writer>=0.400:textproc/p5-XML-Writer \
		p5-YAML>=0:textproc/p5-YAML \
		p5-libwww>=0:www/p5-libwww \
		p5-libxml>=0:textproc/p5-libxml
RUN_DEPENDS:=	${BUILD_DEPENDS}
TEST_DEPENDS=	p5-Test-Most>=0:devel/p5-Test-Most \
		p5-URI>=0:net/p5-URI

USES=		perl5 shebangfix
USE_PERL5=	modbuild
NO_ARCH=	yes
SHEBANG_FILES=	scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl

PORTDATA=	*
PORTDOCS=	*
PORTEXAMPLES=	*

OPTIONS_DEFINE=	DOCS EXAMPLES PGTEST SQLITETEST
PGTEST_DESC=	Test PostGreSQL
SQLITETEST_DESC=	Test SQLite
PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite

post-patch:
	@${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \
		-o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \
		'1s|(/usr)?/bin/perl|${PERL}|'

post-install:
	@${MKDIR} ${STAGEDIR}${DATADIR}
	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR}

post-install-DOCS-on:
	@${MKDIR} ${STAGEDIR}${DOCSDIR}
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md
	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
.endfor
	${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR}

post-install-EXAMPLES-on:
	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}

.include <bsd.port.mk>