head	1.14;
access;
symbols
	RELEASE_8_3_0:1.11
	RELEASE_9_0_0:1.10
	RELEASE_7_4_0:1.10
	RELEASE_8_2_0:1.10
	RELEASE_6_EOL:1.10
	RELEASE_8_1_0:1.10
	RELEASE_7_3_0:1.9
	RELEASE_8_0_0:1.8
	RELEASE_7_2_0:1.6
	RELEASE_7_1_0:1.4
	RELEASE_6_4_0:1.4
	RELEASE_5_EOL:1.4
	RELEASE_7_0_0:1.3
	RELEASE_6_3_0:1.3
	PRE_XORG_7:1.1
	RELEASE_4_EOL:1.1
	RELEASE_6_2_0:1.1;
locks; strict;
comment	@# @;


1.14
date	2012.11.17.05.54.52;	author svnexp;	state Exp;
branches;
next	1.13;

1.13
date	2012.06.30.14.48.28;	author az;	state Exp;
branches;
next	1.12;

1.12
date	2012.06.01.05.16.29;	author dinoex;	state Exp;
branches;
next	1.11;

1.11
date	2012.01.21.17.39.32;	author eadler;	state Exp;
branches;
next	1.10;

1.10
date	2010.03.28.06.31.38;	author dinoex;	state Exp;
branches;
next	1.9;

1.9
date	2010.02.05.11.34.38;	author dinoex;	state Exp;
branches;
next	1.8;

1.8
date	2009.08.02.20.00.08;	author pav;	state Exp;
branches;
next	1.7;

1.7
date	2009.07.31.13.49.18;	author dinoex;	state Exp;
branches;
next	1.6;

1.6
date	2009.03.19.20.54.05;	author miwi;	state Exp;
branches;
next	1.5;

1.5
date	2009.01.15.22.47.02;	author pav;	state Exp;
branches;
next	1.4;

1.4
date	2008.04.17.14.24.11;	author araujo;	state Exp;
branches;
next	1.3;

1.3
date	2007.09.08.00.53.11;	author linimon;	state Exp;
branches;
next	1.2;

1.2
date	2007.05.19.20.00.25;	author flz;	state Exp;
branches;
next	1.1;

1.1
date	2006.05.02.21.30.08;	author garga;	state Exp;
branches;
next	;


desc
@@


1.14
log
@Switch exporter over
@
text
@# New ports collection makefile for:	p5-bioperl-run
# Date created:		21 February 2006
# Whom:	      		Mauricio Herrera Cuadra <mauricio@@arareko.net>
#
# $FreeBSD: head/biology/p5-bioperl-run/Makefile 300895 2012-07-14 12:56:14Z beat $
#

PORTNAME=	bioperl-run
PORTVERSION=	1.6.1
PORTREVISION=	4
CATEGORIES=	biology perl5
MASTER_SITES=	http://bioperl.org/DIST/ \
		CPAN
PKGNAMEPREFIX=	p5-
DISTNAME=	BioPerl-run-${PORTVERSION}

MAINTAINER=	mauricio@@arareko.net
COMMENT=	Wrapper modules for common bioinformatics tools

BUILD_DEPENDS=	p5-bioperl>=1.6.0:${PORTSDIR}/biology/p5-bioperl \
		p5-IPC-Run>=0:${PORTSDIR}/devel/p5-IPC-Run \
		p5-Algorithm-Diff>=0:${PORTSDIR}/devel/p5-Algorithm-Diff
RUN_DEPENDS:=	${BUILD_DEPENDS}

CONFLICTS=	p5-bioperl-run-1.[13579]*

PERL_MODBUILD=	YES
WRKSRC=		${WRKDIR}/BioPerl-run-1.6.0

MAN1=	bp_bioperl_application_installer.pl.1 \
	bp_multi_hmmsearch.pl.1 \
	bp_panalysis.pl.1 \
	bp_papplmaker.pl.1 \
	bp_run_neighbor.pl.1 \
	bp_run_protdist.pl.1

MAN3=	Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
	Bio::Tools::Run::Simprot.3 \
	Bio::Tools::Run::Phylo::Phyml.3 \
	Bio::Tools::Run::Phylo::LVB.3 \
	Bio::Tools::Run::Alignment::Amap.3 \
	Bio::Tools::Run::Tmhmm.3 \
	Bio::Tools::Run::TigrAssembler.3 \
	Bio::Tools::Run::Phylo::PAML::Baseml.3 \
	Bio::Installer::Probcons.3 \
	Bio::Tools::Run::Phylo::Phylip::Base.3 \
	Bio::Tools::Run::Alignment::Exonerate.3 \
	Bio::Tools::Run::Alignment::MAFFT.3 \
	Bio::Tools::Run::Alignment::TCoffee.3 \
	Bio::Tools::Run::Alignment::Sim4.3 \
	Bio::Tools::Run::Analysis.3 \
	Bio::Tools::Run::Phylo::PAML::Yn00.3 \
	Bio::Tools::Run::Alignment::Clustalw.3 \
	Bio::Tools::Run::Phylo::Molphy::ProtML.3 \
	Bio::Tools::Run::Phylo::Hyphy::Base.3 \
	Bio::Tools::Run::Meme.3 \
	Bio::Tools::Run::MCS.3 \
	Bio::Tools::Run::Eponine.3 \
	Bio::Tools::Run::Alignment::Kalign.3 \
	Bio::Tools::Run::TribeMCL.3 \
	Bio::Tools::Run::Analysis::soap.3 \
	Bio::Factory::EMBOSS.3 \
	Bio::Installer::Clustalw.3 \
	Bio::Tools::Run::Seg.3 \
	Bio::Tools::Run::Alignment::Probcons.3 \
	Bio::Tools::Run::RepeatMasker.3 \
	Bio::Installer::TCoffee.3 \
	Bio::Tools::Run::AnalysisFactory.3 \
	Bio::Tools::Run::Cap3.3 \
	Bio::Tools::Run::Alignment::Blat.3 \
	Bio::Tools::Run::Phylo::PhyloBase.3 \
	Bio::Tools::Run::Coil.3 \
	Bio::Tools::Run::Promoterwise.3 \
	Bio::Tools::Run::Alignment::Pal2Nal.3 \
	Bio::Tools::Run::ERPIN.3 \
	Bio::Tools::Run::Phylo::PAML::Evolver.3 \
	Bio::Tools::Run::Phylo::Hyphy::REL.3 \
	Bio::Tools::Run::Genscan.3 \
	Bio::Tools::Run::EMBOSSApplication.3 \
	Bio::Tools::Run::Phylo::Hyphy::Modeltest.3 \
	Bio::Tools::Run::Match.3 \
	Bio::Tools::Run::Phylo::Gumby.3 \
	Bio::Tools::Run::Vista.3 \
	Bio::Tools::Run::Phylo::Hyphy::SLAC.3 \
	Bio::Tools::Run::Mdust.3 \
	Bio::Tools::Run::Alignment::Proda.3 \
	Bio::Installer::SLR.3 \
	Bio::Tools::Run::Primate.3 \
	Bio::Tools::Run::Infernal.3 \
	Bio::Tools::Run::Genemark.3 \
	Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \
	Bio::Tools::Run::EMBOSSacd.3 \
	Bio::Tools::Run::Hmmer.3 \
	Bio::Tools::Run::AnalysisFactory::soap.3 \
	Bio::Tools::Run::Alignment::Lagan.3 \
	Bio::Installer::EMBOSS.3 \
	Bio::Tools::Run::Phrap.3 \
	Bio::Tools::Run::Alignment::Muscle.3 \
	Bio::Tools::Run::tRNAscanSE.3 \
	Bio::Tools::Run::Glimmer.3 \
	Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \
	Bio::Installer::PAML.3 \
	Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \
	Bio::Tools::Run::Phylo::Phast::PhyloFit.3 \
	Bio::Installer::Hyphy.3 \
	Bio::Tools::Run::Phylo::Phast::PhastCons.3 \
	Bio::Tools::Run::Signalp.3 \
	Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \
	Bio::Installer::Generic.3 \
	Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \
	Bio::Tools::Run::Phylo::SLR.3 \
	Bio::Tools::Run::FootPrinter.3 \
	Bio::Tools::Run::Genewise.3 \
	Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \
	Bio::Tools::Run::RNAMotif.3 \
	Bio::Tools::Run::Alignment::StandAloneFasta.3 \
	Bio::Tools::Run::Alignment::Probalign.3 \
	Bio::Tools::Run::Primer3.3 \
	Bio::Tools::Run::Profile.3 \
	Bio::Tools::Run::Phylo::Njtree::Best.3 \
	Bio::Tools::Run::Phylo::QuickTree.3 \
	Bio::Tools::Run::Pseudowise.3 \
	Bio::Tools::Run::Alignment::DBA.3 \
	Bio::Tools::Run::Phylo::Phylip::Consense.3 \
	Bio::Tools::Run::Phylo::Semphy.3 \
	Bio::Tools::Run::Ensembl.3 \
	Bio::Tools::Run::Phylo::Gerp.3 \
	Bio::Tools::Run::Phylo::PAML::Codeml.3 \
	Bio::Installer::Muscle.3 \
	Bio::Tools::Run::Prints.3 \
	Bio::Tools::Run::Phylo::Hyphy::FEL.3

# now install all extra stuff (docs, examples, scripts)
post-install:
	${MKDIR} ${DATADIR}
	@@${CP} -Rv ${WRKSRC}/scripts ${DATADIR}
.if !defined(NOPORTDOCS)
	${MKDIR} ${DOCSDIR}
.for doc in AUTHORS Changes INSTALL.PROGRAMS README
	${INSTALL_DATA} ${WRKSRC}/${doc} ${DOCSDIR}
.endfor
.endif

.include <bsd.port.mk>
@


1.13
log
@- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@@ (bapt@@)
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.12
log
@- update png to 1.5.10
@
text
@d21 2
a22 2
		${SITE_PERL}/IPC/Run.pm:${PORTSDIR}/devel/p5-IPC-Run \
		${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
@


1.11
log
@At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450
ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are
currently broken. This is a temporary measure until we organically stop using
:= or someone(s) spend a lot of time changing all the ports over.

Explicit duplication > := > = and this just moves ports one step to the left

Approved by:	portmgr
@
text
@d10 1
a10 1
PORTREVISION=	3
@


1.10
log
@- update to 1.4.1
Reviewed by:	exp8 run on pointyhat
Supported by:	miwi
@
text
@d23 1
a23 1
RUN_DEPENDS=	${BUILD_DEPENDS}
@


1.9
log
@- update to jpeg-8
@
text
@d10 1
a10 1
PORTREVISION=	2
@


1.8
log
@- Relax check on bioperl version; people keep forgetting to update this check
  when updating bioperl port

Reported by:	pointyhat
@
text
@d10 1
a10 1
PORTREVISION=	1
@


1.7
log
@- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated
Requested by:	edwin
@
text
@d20 1
a20 1
BUILD_DEPENDS=	p5-bioperl=1.6.0:${PORTSDIR}/biology/p5-bioperl \
@


1.6
log
@- Update to 1.6.1

PR:		132122
Submitted by:	Wen Heping <wenheping@@gmail.com>
Approved by:	maintainer
@
text
@d10 1
@


1.5
log
@- Unbreak after p5-bioperl changed portrevision
@
text
@d9 1
a9 2
PORTVERSION=	1.4
PORTREVISION=	1
d14 1
d19 2
a20 1
BUILD_DEPENDS=	p5-bioperl=1.4_2:${PORTSDIR}/biology/p5-bioperl \
d26 2
a27 1
PERL_CONFIGURE=	YES
d29 102
a130 331
MAN3=		Bio::Factory::EMBOSS.3 \
		Bio::Tools::Run::Alignment::Blat.3 \
		Bio::Tools::Run::Alignment::Clustalw.3 \
		Bio::Tools::Run::Alignment::DBA.3 \
		Bio::Tools::Run::Alignment::Lagan.3 \
		Bio::Tools::Run::Alignment::Sim4.3 \
		Bio::Tools::Run::Alignment::StandAloneFasta.3 \
		Bio::Tools::Run::Alignment::TCoffee.3 \
		Bio::Tools::Run::Analysis.3 \
		Bio::Tools::Run::Analysis::soap.3 \
		Bio::Tools::Run::AnalysisFactory.3 \
		Bio::Tools::Run::AnalysisFactory::Pise.3 \
		Bio::Tools::Run::AnalysisFactory::soap.3 \
		Bio::Tools::Run::Coil.3 \
		Bio::Tools::Run::EMBOSSApplication.3 \
		Bio::Tools::Run::EMBOSSacd.3 \
		Bio::Tools::Run::Eponine.3 \
		Bio::Tools::Run::FootPrinter.3 \
		Bio::Tools::Run::Genewise.3 \
		Bio::Tools::Run::Genscan.3 \
		Bio::Tools::Run::Hmmer.3 \
		Bio::Tools::Run::Hmmpfam.3 \
		Bio::Tools::Run::Mdust.3 \
		Bio::Tools::Run::Phylo::Molphy::ProtML.3 \
		Bio::Tools::Run::Phylo::PAML::Codeml.3 \
		Bio::Tools::Run::Phylo::PAML::Yn00.3 \
		Bio::Tools::Run::Phylo::Phylip::Base.3 \
		Bio::Tools::Run::Phylo::Phylip::Consense.3 \
		Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
		Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \
		Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \
		Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \
		Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \
		Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \
		Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \
		Bio::Tools::Run::PiseApplication.3 \
		Bio::Tools::Run::PiseApplication::CSR.3 \
		Bio::Tools::Run::PiseApplication::Puzzle.3 \
		Bio::Tools::Run::PiseApplication::abiview.3 \
		Bio::Tools::Run::PiseApplication::addquart.3 \
		Bio::Tools::Run::PiseApplication::align2model.3 \
		Bio::Tools::Run::PiseApplication::alistat.3 \
		Bio::Tools::Run::PiseApplication::antigenic.3 \
		Bio::Tools::Run::PiseApplication::assp.3 \
		Bio::Tools::Run::PiseApplication::backtranseq.3 \
		Bio::Tools::Run::PiseApplication::bambe.3 \
		Bio::Tools::Run::PiseApplication::banana.3 \
		Bio::Tools::Run::PiseApplication::bionj.3 \
		Bio::Tools::Run::PiseApplication::biosed.3 \
		Bio::Tools::Run::PiseApplication::bl2seq.3 \
		Bio::Tools::Run::PiseApplication::blast2.3 \
		Bio::Tools::Run::PiseApplication::blimps.3 \
		Bio::Tools::Run::PiseApplication::blimps_block.3 \
		Bio::Tools::Run::PiseApplication::blimps_matrix.3 \
		Bio::Tools::Run::PiseApplication::boxshade.3 \
		Bio::Tools::Run::PiseApplication::btwisted.3 \
		Bio::Tools::Run::PiseApplication::cai.3 \
		Bio::Tools::Run::PiseApplication::cap.3 \
		Bio::Tools::Run::PiseApplication::cds.3 \
		Bio::Tools::Run::PiseApplication::chaos.3 \
		Bio::Tools::Run::PiseApplication::charge.3 \
		Bio::Tools::Run::PiseApplication::checktrans.3 \
		Bio::Tools::Run::PiseApplication::chips.3 \
		Bio::Tools::Run::PiseApplication::cirdna.3 \
		Bio::Tools::Run::PiseApplication::clique.3 \
		Bio::Tools::Run::PiseApplication::clustalw.3 \
		Bio::Tools::Run::PiseApplication::clustalw_convert.3 \
		Bio::Tools::Run::PiseApplication::codcmp.3 \
		Bio::Tools::Run::PiseApplication::coderet.3 \
		Bio::Tools::Run::PiseApplication::codnocod.3 \
		Bio::Tools::Run::PiseApplication::codontree.3 \
		Bio::Tools::Run::PiseApplication::codonw.3 \
		Bio::Tools::Run::PiseApplication::comalign.3 \
		Bio::Tools::Run::PiseApplication::combat.3 \
		Bio::Tools::Run::PiseApplication::compseq.3 \
		Bio::Tools::Run::PiseApplication::con_filter.3 \
		Bio::Tools::Run::PiseApplication::confmat.3 \
		Bio::Tools::Run::PiseApplication::cons.3 \
		Bio::Tools::Run::PiseApplication::consense.3 \
		Bio::Tools::Run::PiseApplication::consensus.3 \
		Bio::Tools::Run::PiseApplication::cpgplot.3 \
		Bio::Tools::Run::PiseApplication::cpgreport.3 \
		Bio::Tools::Run::PiseApplication::cusp.3 \
		Bio::Tools::Run::PiseApplication::cutseq.3 \
		Bio::Tools::Run::PiseApplication::dan.3 \
		Bio::Tools::Run::PiseApplication::dca.3 \
		Bio::Tools::Run::PiseApplication::decorate.3 \
		Bio::Tools::Run::PiseApplication::degapseq.3 \
		Bio::Tools::Run::PiseApplication::descseq.3 \
		Bio::Tools::Run::PiseApplication::dialign2.3 \
		Bio::Tools::Run::PiseApplication::diffseq.3 \
		Bio::Tools::Run::PiseApplication::digest.3 \
		Bio::Tools::Run::PiseApplication::distmat.3 \
		Bio::Tools::Run::PiseApplication::distquart.3 \
		Bio::Tools::Run::PiseApplication::dnadist.3 \
		Bio::Tools::Run::PiseApplication::dnapars.3 \
		Bio::Tools::Run::PiseApplication::dollop.3 \
		Bio::Tools::Run::PiseApplication::domainer.3 \
		Bio::Tools::Run::PiseApplication::dotmatcher.3 \
		Bio::Tools::Run::PiseApplication::dotpath.3 \
		Bio::Tools::Run::PiseApplication::dottup.3 \
		Bio::Tools::Run::PiseApplication::drawgram.3 \
		Bio::Tools::Run::PiseApplication::drawpyr.3 \
		Bio::Tools::Run::PiseApplication::drawtree.3 \
		Bio::Tools::Run::PiseApplication::dreg.3 \
		Bio::Tools::Run::PiseApplication::druid.3 \
		Bio::Tools::Run::PiseApplication::dsc.3 \
		Bio::Tools::Run::PiseApplication::dssp.3 \
		Bio::Tools::Run::PiseApplication::einverted.3 \
		Bio::Tools::Run::PiseApplication::emma.3 \
		Bio::Tools::Run::PiseApplication::emowse.3 \
		Bio::Tools::Run::PiseApplication::environ.3 \
		Bio::Tools::Run::PiseApplication::eprimer3.3 \
		Bio::Tools::Run::PiseApplication::equicktandem.3 \
		Bio::Tools::Run::PiseApplication::est2genome.3 \
		Bio::Tools::Run::PiseApplication::etandem.3 \
		Bio::Tools::Run::PiseApplication::extractfeat.3 \
		Bio::Tools::Run::PiseApplication::extractseq.3 \
		Bio::Tools::Run::PiseApplication::fasta.3 \
		Bio::Tools::Run::PiseApplication::fastdnaml.3 \
		Bio::Tools::Run::PiseApplication::fastrna.3 \
		Bio::Tools::Run::PiseApplication::filtersites.3 \
		Bio::Tools::Run::PiseApplication::findkm.3 \
		Bio::Tools::Run::PiseApplication::fitch.3 \
		Bio::Tools::Run::PiseApplication::fmtseq.3 \
		Bio::Tools::Run::PiseApplication::freak.3 \
		Bio::Tools::Run::PiseApplication::fuzznuc.3 \
		Bio::Tools::Run::PiseApplication::fuzzpro.3 \
		Bio::Tools::Run::PiseApplication::fuzztran.3 \
		Bio::Tools::Run::PiseApplication::gb2xml.3 \
		Bio::Tools::Run::PiseApplication::geecee.3 \
		Bio::Tools::Run::PiseApplication::genscan.3 \
		Bio::Tools::Run::PiseApplication::getblock.3 \
		Bio::Tools::Run::PiseApplication::getorf.3 \
		Bio::Tools::Run::PiseApplication::gff2ps.3 \
		Bio::Tools::Run::PiseApplication::gibbs.3 \
		Bio::Tools::Run::PiseApplication::gibbs_scan.3 \
		Bio::Tools::Run::PiseApplication::golden.3 \
		Bio::Tools::Run::PiseApplication::grailclnt.3 \
		Bio::Tools::Run::PiseApplication::gruppi.3 \
		Bio::Tools::Run::PiseApplication::helixturnhelix.3 \
		Bio::Tools::Run::PiseApplication::hmmalign.3 \
		Bio::Tools::Run::PiseApplication::hmmbuild.3 \
		Bio::Tools::Run::PiseApplication::hmmcalibrate.3 \
		Bio::Tools::Run::PiseApplication::hmmconvert.3 \
		Bio::Tools::Run::PiseApplication::hmmemit.3 \
		Bio::Tools::Run::PiseApplication::hmmer2sam.3 \
		Bio::Tools::Run::PiseApplication::hmmfetch.3 \
		Bio::Tools::Run::PiseApplication::hmmpfam.3 \
		Bio::Tools::Run::PiseApplication::hmmscore.3 \
		Bio::Tools::Run::PiseApplication::hmmsearch.3 \
		Bio::Tools::Run::PiseApplication::hmoment.3 \
		Bio::Tools::Run::PiseApplication::homology.3 \
		Bio::Tools::Run::PiseApplication::html4blast.3 \
		Bio::Tools::Run::PiseApplication::iep.3 \
		Bio::Tools::Run::PiseApplication::infoalign.3 \
		Bio::Tools::Run::PiseApplication::infoseq.3 \
		Bio::Tools::Run::PiseApplication::interface.3 \
		Bio::Tools::Run::PiseApplication::isochore.3 \
		Bio::Tools::Run::PiseApplication::kitsch.3 \
		Bio::Tools::Run::PiseApplication::lassap.3 \
		Bio::Tools::Run::PiseApplication::lgicsearch.3 \
		Bio::Tools::Run::PiseApplication::lindna.3 \
		Bio::Tools::Run::PiseApplication::listor.3 \
		Bio::Tools::Run::PiseApplication::loadseq.3 \
		Bio::Tools::Run::PiseApplication::lvb.3 \
		Bio::Tools::Run::PiseApplication::makehist.3 \
		Bio::Tools::Run::PiseApplication::map.3 \
		Bio::Tools::Run::PiseApplication::marscan.3 \
		Bio::Tools::Run::PiseApplication::maskfeat.3 \
		Bio::Tools::Run::PiseApplication::maskseq.3 \
		Bio::Tools::Run::PiseApplication::matcher.3 \
		Bio::Tools::Run::PiseApplication::megamerger.3 \
		Bio::Tools::Run::PiseApplication::melting.3 \
		Bio::Tools::Run::PiseApplication::merger.3 \
		Bio::Tools::Run::PiseApplication::mfold.3 \
		Bio::Tools::Run::PiseApplication::mix.3 \
		Bio::Tools::Run::PiseApplication::modelfromalign.3 \
		Bio::Tools::Run::PiseApplication::most.3 \
		Bio::Tools::Run::PiseApplication::mreps.3 \
		Bio::Tools::Run::PiseApplication::msa.3 \
		Bio::Tools::Run::PiseApplication::msbar.3 \
		Bio::Tools::Run::PiseApplication::mspcrunch.3 \
		Bio::Tools::Run::PiseApplication::mview_alig.3 \
		Bio::Tools::Run::PiseApplication::mview_blast.3 \
		Bio::Tools::Run::PiseApplication::mwfilter.3 \
		Bio::Tools::Run::PiseApplication::needle.3 \
		Bio::Tools::Run::PiseApplication::neighbor.3 \
		Bio::Tools::Run::PiseApplication::newcpgreport.3 \
		Bio::Tools::Run::PiseApplication::newcpgseek.3 \
		Bio::Tools::Run::PiseApplication::newseq.3 \
		Bio::Tools::Run::PiseApplication::njdist.3 \
		Bio::Tools::Run::PiseApplication::nnssp.3 \
		Bio::Tools::Run::PiseApplication::notseq.3 \
		Bio::Tools::Run::PiseApplication::nrscope.3 \
		Bio::Tools::Run::PiseApplication::nthseq.3 \
		Bio::Tools::Run::PiseApplication::octanol.3 \
		Bio::Tools::Run::PiseApplication::oddcomp.3 \
		Bio::Tools::Run::PiseApplication::palindrome.3 \
		Bio::Tools::Run::PiseApplication::pam.3 \
		Bio::Tools::Run::PiseApplication::parciquart.3 \
		Bio::Tools::Run::PiseApplication::pars.3 \
		Bio::Tools::Run::PiseApplication::pasteseq.3 \
		Bio::Tools::Run::PiseApplication::patmatdb.3 \
		Bio::Tools::Run::PiseApplication::patmatmotifs.3 \
		Bio::Tools::Run::PiseApplication::patser.3 \
		Bio::Tools::Run::PiseApplication::pdbsearch.3 \
		Bio::Tools::Run::PiseApplication::pepcoil.3 \
		Bio::Tools::Run::PiseApplication::pepinfo.3 \
		Bio::Tools::Run::PiseApplication::pepnet.3 \
		Bio::Tools::Run::PiseApplication::pepstats.3 \
		Bio::Tools::Run::PiseApplication::pepwheel.3 \
		Bio::Tools::Run::PiseApplication::pepwindow.3 \
		Bio::Tools::Run::PiseApplication::pepwindowall.3 \
		Bio::Tools::Run::PiseApplication::pestfind.3 \
		Bio::Tools::Run::PiseApplication::pftools.3 \
		Bio::Tools::Run::PiseApplication::phiblast.3 \
		Bio::Tools::Run::PiseApplication::pima.3 \
		Bio::Tools::Run::PiseApplication::plotcon.3 \
		Bio::Tools::Run::PiseApplication::plotorf.3 \
		Bio::Tools::Run::PiseApplication::plsearch.3 \
		Bio::Tools::Run::PiseApplication::polydot.3 \
		Bio::Tools::Run::PiseApplication::pratt.3 \
		Bio::Tools::Run::PiseApplication::predator.3 \
		Bio::Tools::Run::PiseApplication::preg.3 \
		Bio::Tools::Run::PiseApplication::prettyalign.3 \
		Bio::Tools::Run::PiseApplication::prettyplot.3 \
		Bio::Tools::Run::PiseApplication::prettyseq.3 \
		Bio::Tools::Run::PiseApplication::primersearch.3 \
		Bio::Tools::Run::PiseApplication::primo.3 \
		Bio::Tools::Run::PiseApplication::prodom.3 \
		Bio::Tools::Run::PiseApplication::profit.3 \
		Bio::Tools::Run::PiseApplication::prophecy.3 \
		Bio::Tools::Run::PiseApplication::prophet.3 \
		Bio::Tools::Run::PiseApplication::prose.3 \
		Bio::Tools::Run::PiseApplication::prot_nucml.3 \
		Bio::Tools::Run::PiseApplication::protal2dna.3 \
		Bio::Tools::Run::PiseApplication::protdist.3 \
		Bio::Tools::Run::PiseApplication::protpars.3 \
		Bio::Tools::Run::PiseApplication::pscan.3 \
		Bio::Tools::Run::PiseApplication::psiblast.3 \
		Bio::Tools::Run::PiseApplication::psort2.3 \
		Bio::Tools::Run::PiseApplication::pyramids.3 \
		Bio::Tools::Run::PiseApplication::pyreval.3 \
		Bio::Tools::Run::PiseApplication::qstar.3 \
		Bio::Tools::Run::PiseApplication::quicktree.3 \
		Bio::Tools::Run::PiseApplication::readnexus.3 \
		Bio::Tools::Run::PiseApplication::readseq.3 \
		Bio::Tools::Run::PiseApplication::recoder.3 \
		Bio::Tools::Run::PiseApplication::redata.3 \
		Bio::Tools::Run::PiseApplication::remap.3 \
		Bio::Tools::Run::PiseApplication::repeats.3 \
		Bio::Tools::Run::PiseApplication::restover.3 \
		Bio::Tools::Run::PiseApplication::restrict.3 \
		Bio::Tools::Run::PiseApplication::revseq.3 \
		Bio::Tools::Run::PiseApplication::rnadistance.3 \
		Bio::Tools::Run::PiseApplication::rnaeval.3 \
		Bio::Tools::Run::PiseApplication::rnafold.3 \
		Bio::Tools::Run::PiseApplication::rnaga.3 \
		Bio::Tools::Run::PiseApplication::rnaheat.3 \
		Bio::Tools::Run::PiseApplication::rnainverse.3 \
		Bio::Tools::Run::PiseApplication::rnapdist.3 \
		Bio::Tools::Run::PiseApplication::rnasubopt.3 \
		Bio::Tools::Run::PiseApplication::sam2hmmer.3 \
		Bio::Tools::Run::PiseApplication::sampleseqs.3 \
		Bio::Tools::Run::PiseApplication::saps.3 \
		Bio::Tools::Run::PiseApplication::satellites.3 \
		Bio::Tools::Run::PiseApplication::scan_for_matches.3 \
		Bio::Tools::Run::PiseApplication::scope.3 \
		Bio::Tools::Run::PiseApplication::scopparse.3 \
		Bio::Tools::Run::PiseApplication::seqboot.3 \
		Bio::Tools::Run::PiseApplication::seqgen.3 \
		Bio::Tools::Run::PiseApplication::seqmatchall.3 \
		Bio::Tools::Run::PiseApplication::seqsblast.3 \
		Bio::Tools::Run::PiseApplication::seqstat.3 \
		Bio::Tools::Run::PiseApplication::showalign.3 \
		Bio::Tools::Run::PiseApplication::showfeat.3 \
		Bio::Tools::Run::PiseApplication::showorf.3 \
		Bio::Tools::Run::PiseApplication::showseq.3 \
		Bio::Tools::Run::PiseApplication::shuffleseq.3 \
		Bio::Tools::Run::PiseApplication::sigcleave.3 \
		Bio::Tools::Run::PiseApplication::siggen.3 \
		Bio::Tools::Run::PiseApplication::sigscan.3 \
		Bio::Tools::Run::PiseApplication::silent.3 \
		Bio::Tools::Run::PiseApplication::sirna.3 \
		Bio::Tools::Run::PiseApplication::splitter.3 \
		Bio::Tools::Run::PiseApplication::sreformat.3 \
		Bio::Tools::Run::PiseApplication::stretcher.3 \
		Bio::Tools::Run::PiseApplication::stride.3 \
		Bio::Tools::Run::PiseApplication::stssearch.3 \
		Bio::Tools::Run::PiseApplication::supermatcher.3 \
		Bio::Tools::Run::PiseApplication::syco.3 \
		Bio::Tools::Run::PiseApplication::tacg.3 \
		Bio::Tools::Run::PiseApplication::tfscan.3 \
		Bio::Tools::Run::PiseApplication::tipdate.3 \
		Bio::Tools::Run::PiseApplication::tmap.3 \
		Bio::Tools::Run::PiseApplication::toppred.3 \
		Bio::Tools::Run::PiseApplication::tranalign.3 \
		Bio::Tools::Run::PiseApplication::transeq.3 \
		Bio::Tools::Run::PiseApplication::treealign.3 \
		Bio::Tools::Run::PiseApplication::trimest.3 \
		Bio::Tools::Run::PiseApplication::trimseq.3 \
		Bio::Tools::Run::PiseApplication::trnascan.3 \
		Bio::Tools::Run::PiseApplication::twofeat.3 \
		Bio::Tools::Run::PiseApplication::unroot.3 \
		Bio::Tools::Run::PiseApplication::vectorstrip.3 \
		Bio::Tools::Run::PiseApplication::water.3 \
		Bio::Tools::Run::PiseApplication::weighbor.3 \
		Bio::Tools::Run::PiseApplication::whichdb.3 \
		Bio::Tools::Run::PiseApplication::wise2.3 \
		Bio::Tools::Run::PiseApplication::wobble.3 \
		Bio::Tools::Run::PiseApplication::wordcount.3 \
		Bio::Tools::Run::PiseApplication::wordmatch.3 \
		Bio::Tools::Run::PiseApplication::wublast2.3 \
		Bio::Tools::Run::PiseApplication::xblast.3 \
		Bio::Tools::Run::PiseApplication::xpound.3 \
		Bio::Tools::Run::PiseJob.3 \
		Bio::Tools::Run::PiseJobParser.3 \
		Bio::Tools::Run::PiseWorkflow.3 \
		Bio::Tools::Run::Primate.3 \
		Bio::Tools::Run::Primer3.3 \
		Bio::Tools::Run::Prints.3 \
		Bio::Tools::Run::Profile.3 \
		Bio::Tools::Run::Promoterwise.3 \
		Bio::Tools::Run::Pseudowise.3 \
		Bio::Tools::Run::RepeatMasker.3 \
		Bio::Tools::Run::Seg.3 \
		Bio::Tools::Run::Signalp.3 \
		Bio::Tools::Run::Tmhmm.3 \
		Bio::Tools::Run::TribeMCL.3 \
		Bio::Tools::Run::Vista.3
a135 2
	${MKDIR} ${EXAMPLESDIR}
	@@${CP} -Rv ${WRKSRC}/examples/* ${EXAMPLESDIR}
@


1.4
log
@- Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN.

PR:		ports/122674
Submitted by:	Philip M. Gollucci <pgollucci@@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	portmgr (pav)
@
text
@d19 1
a19 1
BUILD_DEPENDS=	p5-bioperl=1.4_1:${PORTSDIR}/biology/p5-bioperl \
@


1.3
log
@Welcome bsd.perl.mk.  Add support for constructs such as USE_PERL5=5.8.0+.
Drop support for antique perl.

Work done by:	gabor
Sponsored by:	Google Summer of Code 2007
Hat:		portmgr
@
text
@d13 1
a13 1
		${MASTER_SITE_PERL_CPAN}
@


1.2
log
@- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
@
text
@a358 6
.include <bsd.port.pre.mk>

.if ${PERL_LEVEL} < 500600
IGNORE=		requires Perl 5.6 or better
.endif

d372 1
a372 1
.include <bsd.port.post.mk>
@


1.1
log
@Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93674
Submitted by:	Mauricio Herrera Cuadra <mauricio@@arareko.net>
@
text
@d10 1
d19 1
a19 1
BUILD_DEPENDS=	p5-bioperl=1.4:${PORTSDIR}/biology/p5-bioperl \
@

