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

PORTNAME=	bioperl
PORTVERSION=	1.6.924
PORTREVISION=	4
CATEGORIES=	biology perl5
MASTER_SITES=	CPAN
MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
PKGNAMEPREFIX=	p5-
DISTNAME=	BioPerl-${PORTVERSION}

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

LICENSE=	ART10 GPLv1
LICENSE_COMB=	dual

BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \
		p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \
		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \
		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
		p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \
		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
		p5-Error>=0:${PORTSDIR}/lang/p5-Error \
		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
		p5-GD-SVG>=0:${PORTSDIR}/graphics/p5-GD-SVG \
		p5-Graph>=0:${PORTSDIR}/math/p5-Graph \
		p5-GraphViz>=0:${PORTSDIR}/graphics/p5-GraphViz \
		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
		p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \
		p5-IO-stringy>=0:${PORTSDIR}/devel/p5-IO-stringy \
		p5-IO-String>=0:${PORTSDIR}/devel/p5-IO-String \
		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
		p5-SOAP-Lite>=0:${PORTSDIR}/net/p5-SOAP-Lite \
		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
		p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \
		p5-Spreadsheet-ParseExcel>=0:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
		p5-SVG>=0:${PORTSDIR}/textproc/p5-SVG \
		p5-SVG-Graph>=0:${PORTSDIR}/graphics/p5-SVG-Graph \
		p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \
		p5-Text-Shellwords>=0:${PORTSDIR}/textproc/p5-Text-Shellwords \
		p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \
		p5-URI>=0:${PORTSDIR}/net/p5-URI \
		p5-XML-DOM>=0:${PORTSDIR}/textproc/p5-XML-DOM \
		p5-XML-DOM-XPath>=0:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
		p5-XML-LibXML>=0:${PORTSDIR}/textproc/p5-XML-LibXML \
		p5-XML-Parser>=0:${PORTSDIR}/textproc/p5-XML-Parser \
		p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \
		p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
		p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \
		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
		p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \
		p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \
		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
		p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml

RUN_DEPENDS:=	${BUILD_DEPENDS}

USES=		perl5 shebangfix
USE_PERL5=	modbuild
NO_ARCH=	yes

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

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

post-install:
	@${MKDIR} ${STAGEDIR}${DATADIR}
	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR}
	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
	@${MKDIR} ${STAGEDIR}${DOCSDIR}
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
	${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
.endfor
	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}

.include <bsd.port.mk>
pendabot/npm_and_yarn/devel/electron6/files/lodash.merge-4.6.2'>dependabot/npm_and_yarn/devel/electron6/files/lodash.merge-4.6.2</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/node-fetch-2.6.1'>dependabot/npm_and_yarn/devel/electron6/files/node-fetch-2.6.1</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/serve-10.1.2'>dependabot/npm_and_yarn/devel/electron6/files/serve-10.1.2</option>
<option value='gnome-3.22'>gnome-3.22</option>
<option value='gnome-3.24'>gnome-3.24</option>
<option value='gnome-3.26'>gnome-3.26</option>
<option value='gnome-3.28'>gnome-3.28</option>
<option value='gnome-3.32'>gnome-3.32</option>
<option value='gnome-3.36'>gnome-3.36</option>
<option value='gstreamer'>gstreamer</option>
<option value='gstreamer-1.16'>gstreamer-1.16</option>
<option value='gstreamer0.10-removal'>gstreamer0.10-removal</option>
<option value='main' selected='selected'>main</option>
<option value='master'>master</option>
<option value='mate-1.16'>mate-1.16</option>
<option value='mate-1.18'>mate-1.18</option>
<option value='mate-1.20'>mate-1.20</option>
<option value='mate-1.22'>mate-1.22</option>
</select> <input type='submit' value='switch'/></form></td></tr>
<tr><td class='sub'>FreeBSD GNOME current development ports (https://github.com/freebsd/freebsd-ports-gnome)</td><td class='sub right'></td></tr></table>
<table class='tabs'><tr><td>
<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/about/'>about</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/'>summary</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/refs/?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>refs</a><a class='active' href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/mail/drac/pkg-descr'>log</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/tree/mail/drac/pkg-descr?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>tree</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/mail/drac/pkg-descr?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>commit</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/diff/mail/drac/pkg-descr?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>diff</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/stats/mail/drac/pkg-descr'>stats</a></td><td class='form'><form class='right' method='get' action='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/mail/drac/pkg-descr'>
<input type='hidden' name='id' value='c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'/><select name='qt'>
<option value='grep'>log msg</option>
<option value='author'>author</option>
<option value='committer'>committer</option>
<option value='range'>range</option>
</select>
<input class='txt' type='search' size='10' name='q' value=''/>
<input type='submit' value='search'/>
</form>
</td></tr></table>
<div class='path'>path: <a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>root</a>/<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/mail?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>mail</a>/<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/mail/drac?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>drac</a>/<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/mail/drac/pkg-descr?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6'>pkg-descr</a></div><div class='content'><table class='list nowrap'><tr class='nohover'><th></th><th class='left'>Commit message (<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/mail/drac/pkg-descr?id=c4870479d9e0eeb6b223fc42e5f1cf7caa8511a6&amp;showmsg=1'>Expand</a>)</th><th class='left'>Author</th><th class='left'>Age</th><th class='left'>Files</th><th class='left'>Lines</th></tr>