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Date:      Tue, 21 Feb 2006 19:49:05 GMT
From:      Mauricio Herrera Cuadra <mauricio@arareko.net>
To:        freebsd-gnats-submit@FreeBSD.org
Subject:   ports/93675: New port: biology/p5-bioperl-run-devel Wrapper modules for common bioinformatics tools (developer release)
Message-ID:  <200602211949.k1LJn5XJ015353@www.freebsd.org>
Resent-Message-ID: <200602211950.k1LJo37J017446@freefall.freebsd.org>

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>Number:         93675
>Category:       ports
>Synopsis:       New port: biology/p5-bioperl-run-devel Wrapper modules for common bioinformatics tools (developer release)
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Tue Feb 21 19:50:02 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator:     Mauricio Herrera Cuadra
>Release:        FreeBSD 5.5-PRERELEASE i386
>Organization:
>Environment:
FreeBSD nordwand.arareko.net 5.5-PRERELEASE FreeBSD 5.5-PRERELEASE #0: Wed Feb  1 22:39:13 CST 2006     root@nordwand.arareko.net:/usr/obj/usr/src/sys/nordwand  i386

>Description:
              This port installs the developer release (1.5.1) of the Bioperl-run distribution.
>How-To-Repeat:
              
>Fix:
              # This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	biology/p5-bioperl-run-devel
#	biology/p5-bioperl-run-devel/pkg-plist
#	biology/p5-bioperl-run-devel/pkg-descr
#	biology/p5-bioperl-run-devel/distinfo
#	biology/p5-bioperl-run-devel/Makefile
#
echo c - biology/p5-bioperl-run-devel
mkdir -p biology/p5-bioperl-run-devel > /dev/null 2>&1
echo x - biology/p5-bioperl-run-devel/pkg-plist
sed 's/^X//' >biology/p5-bioperl-run-devel/pkg-plist << 'END-of-biology/p5-bioperl-run-devel/pkg-plist'
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X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showalign.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showfeat.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showorf.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showseq.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/shuffleseq.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigcleave.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/siggen.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigscan.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/silent.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sirna.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/splitter.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sreformat.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stretcher.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stride.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stssearch.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/supermatcher.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/syco.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tacg.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tfscan.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tipdate.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tmap.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/toppred.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tranalign.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/transeq.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/treealign.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimest.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimseq.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trnascan.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/twofeat.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/unroot.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/vectorstrip.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/water.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/weighbor.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/whichdb.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wise2.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wobble.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordcount.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordmatch.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wublast2.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xblast.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xpound.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseJob.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseJobParser.pm
X%%SITE_PERL%%/Bio/Tools/Run/PiseWorkflow.pm
X%%SITE_PERL%%/Bio/Tools/Run/Primate.pm
X%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
X%%SITE_PERL%%/Bio/Tools/Run/Prints.pm
X%%SITE_PERL%%/Bio/Tools/Run/Profile.pm
X%%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm
X%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
X%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
X%%SITE_PERL%%/Bio/Tools/Run/Seg.pm
X%%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
X%%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
X%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
X%%SITE_PERL%%/Bio/Tools/Run/Vista.pm
X%%DATADIR%%/scripts/bioperl_application_installer.PLS
X%%DATADIR%%/scripts/panalysis.PLS
X%%DATADIR%%/scripts/papplmaker.PLS
X%%DATADIR%%/scripts/run_neighbor.PLS
X%%DATADIR%%/scripts/run_protdist.PLS
X%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
X%%PORTDOCS%%%%DOCSDIR%%/Changes
X%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
X%%PORTDOCS%%%%DOCSDIR%%/README
X%%EXAMPLESDIR%%/pise/blast-kun.pl
X%%EXAMPLESDIR%%/pise/blast2.pl
X%%EXAMPLESDIR%%/pise/clustalw.pl
X%%EXAMPLESDIR%%/pise/dnadist.data
X%%EXAMPLESDIR%%/pise/dnadist.pl
X%%EXAMPLESDIR%%/pise/genscan.pl
X%%EXAMPLESDIR%%/pise/needle.pl
X%%EXAMPLESDIR%%/pise/phylo-kun.pl
X%%EXAMPLESDIR%%/pise/toppred.pl
X@dirrm %%EXAMPLESDIR%%/pise
X@dirrm %%EXAMPLESDIR%%
X%%PORTDOCS%%@dirrm %%DOCSDIR%%
X@dirrm %%DATADIR%%/scripts
X@dirrm %%DATADIR%%
X@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/PiseApplication
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Forester
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Analysis
X@dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment
X@dirrmtry %%SITE_PERL%%/Bio/Tools/Run
X@dirrmtry %%SITE_PERL%%/Bio/Tools
X@dirrm %%SITE_PERL%%/Bio/Installer
X@dirrmtry %%SITE_PERL%%/Bio/Factory
X@dirrmtry %%SITE_PERL%%/Bio
END-of-biology/p5-bioperl-run-devel/pkg-plist
echo x - biology/p5-bioperl-run-devel/pkg-descr
sed 's/^X//' >biology/p5-bioperl-run-devel/pkg-descr << 'END-of-biology/p5-bioperl-run-devel/pkg-descr'
XBioperl-run contain modules that provides a PERL interface to various
Xbioinformatics applications. This allows various applications to be used
Xwith common Bioperl objects.
X
XWWW: http://bioperl.org/
END-of-biology/p5-bioperl-run-devel/pkg-descr
echo x - biology/p5-bioperl-run-devel/distinfo
sed 's/^X//' >biology/p5-bioperl-run-devel/distinfo << 'END-of-biology/p5-bioperl-run-devel/distinfo'
XMD5 (bioperl-run-1.5.1.tar.gz) = dbfce41fa5d86dab5fd1d6af4196c646
XSHA256 (bioperl-run-1.5.1.tar.gz) = d9e1f5bdff5541376cab1c8b7e8db9bedbbb7b6f76b965d55dc20122a98f93e8
XSIZE (bioperl-run-1.5.1.tar.gz) = 864369
END-of-biology/p5-bioperl-run-devel/distinfo
echo x - biology/p5-bioperl-run-devel/Makefile
sed 's/^X//' >biology/p5-bioperl-run-devel/Makefile << 'END-of-biology/p5-bioperl-run-devel/Makefile'
X# New ports collection makefile for:	biology/p5-bioperl-run-devel
X# Date created:		21 February 2006
X# Whom:	      		Mauricio Herrera Cuadra <mauricio@arareko.net>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	bioperl-run
XPORTVERSION=	1.5.1
XCATEGORIES=	biology perl5
XMASTER_SITES=	http://bioperl.org/DIST/
XPKGNAMEPREFIX=	p5-
X
XMAINTAINER=	mauricio@arareko.net
XCOMMENT=	Wrapper modules for common bioinformatics tools (developer release)
X
XBUILD_DEPENDS=	p5-bioperl=1.5.1:${PORTSDIR}/biology/p5-bioperl-devel \
X		${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
XRUN_DEPENDS=	${BUILD_DEPENDS}
X
XCONFLICTS=	p5-bioperl-run-1.[02468]*
X
XLATEST_LINK=	p5-bioperl-run-devel
X
XPERL_CONFIGURE=	YES
X
XMAN3=		Bio::Factory::EMBOSS.3 \
X		Bio::Installer::Clustalw.3 \
X		Bio::Installer::EMBOSS.3 \
X		Bio::Installer::Generic.3 \
X		Bio::Installer::PAML.3 \
X		Bio::Installer::Probcons.3 \
X		Bio::Installer::TCoffee.3 \
X		Bio::Tools::Run::AbstractRunner.3 \
X		Bio::Tools::Run::Alignment::Blat.3 \
X		Bio::Tools::Run::Alignment::Clustalw.3 \
X		Bio::Tools::Run::Alignment::DBA.3 \
X		Bio::Tools::Run::Alignment::Exonerate.3 \
X		Bio::Tools::Run::Alignment::Lagan.3 \
X		Bio::Tools::Run::Alignment::MAFFT.3 \
X		Bio::Tools::Run::Alignment::Muscle.3 \
X		Bio::Tools::Run::Alignment::Probcons.3 \
X		Bio::Tools::Run::Alignment::Sim4.3 \
X		Bio::Tools::Run::Alignment::StandAloneFasta.3 \
X		Bio::Tools::Run::Alignment::TCoffee.3 \
X		Bio::Tools::Run::Analysis.3 \
X		Bio::Tools::Run::Analysis::soap.3 \
X		Bio::Tools::Run::AnalysisFactory.3 \
X		Bio::Tools::Run::AnalysisFactory::Pise.3 \
X		Bio::Tools::Run::AnalysisFactory::soap.3 \
X		Bio::Tools::Run::Coil.3 \
X		Bio::Tools::Run::EMBOSSApplication.3 \
X		Bio::Tools::Run::EMBOSSacd.3 \
X		Bio::Tools::Run::Eponine.3 \
X		Bio::Tools::Run::FootPrinter.3 \
X		Bio::Tools::Run::Genewise.3 \
X		Bio::Tools::Run::Genscan.3 \
X		Bio::Tools::Run::Hmmer.3 \
X		Bio::Tools::Run::JavaRunner.3 \
X		Bio::Tools::Run::Mdust.3 \
X		Bio::Tools::Run::Phrap.3 \
X		Bio::Tools::Run::Phylo::Forester::SDI.3 \
X		Bio::Tools::Run::Phylo::LVB.3 \
X		Bio::Tools::Run::Phylo::Molphy::ProtML.3 \
X		Bio::Tools::Run::Phylo::PAML::Baseml.3 \
X		Bio::Tools::Run::Phylo::PAML::Codeml.3 \
X		Bio::Tools::Run::Phylo::PAML::Yn00.3 \
X		Bio::Tools::Run::Phylo::Phylip::Base.3 \
X		Bio::Tools::Run::Phylo::Phylip::Consense.3 \
X		Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
X		Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \
X		Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \
X		Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \
X		Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \
X		Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \
X		Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \
X		Bio::Tools::Run::PiseApplication.3 \
X		Bio::Tools::Run::PiseApplication::CSR.3 \
X		Bio::Tools::Run::PiseApplication::Puzzle.3 \
X		Bio::Tools::Run::PiseApplication::abiview.3 \
X		Bio::Tools::Run::PiseApplication::addquart.3 \
X		Bio::Tools::Run::PiseApplication::align2model.3 \
X		Bio::Tools::Run::PiseApplication::alistat.3 \
X		Bio::Tools::Run::PiseApplication::antigenic.3 \
X		Bio::Tools::Run::PiseApplication::assp.3 \
X		Bio::Tools::Run::PiseApplication::backtranseq.3 \
X		Bio::Tools::Run::PiseApplication::bambe.3 \
X		Bio::Tools::Run::PiseApplication::banana.3 \
X		Bio::Tools::Run::PiseApplication::bionj.3 \
X		Bio::Tools::Run::PiseApplication::biosed.3 \
X		Bio::Tools::Run::PiseApplication::bl2seq.3 \
X		Bio::Tools::Run::PiseApplication::blast2.3 \
X		Bio::Tools::Run::PiseApplication::blimps.3 \
X		Bio::Tools::Run::PiseApplication::blimps_block.3 \
X		Bio::Tools::Run::PiseApplication::blimps_matrix.3 \
X		Bio::Tools::Run::PiseApplication::boxshade.3 \
X		Bio::Tools::Run::PiseApplication::btwisted.3 \
X		Bio::Tools::Run::PiseApplication::cai.3 \
X		Bio::Tools::Run::PiseApplication::cap.3 \
X		Bio::Tools::Run::PiseApplication::cds.3 \
X		Bio::Tools::Run::PiseApplication::chaos.3 \
X		Bio::Tools::Run::PiseApplication::charge.3 \
X		Bio::Tools::Run::PiseApplication::checktrans.3 \
X		Bio::Tools::Run::PiseApplication::chips.3 \
X		Bio::Tools::Run::PiseApplication::cirdna.3 \
X		Bio::Tools::Run::PiseApplication::clique.3 \
X		Bio::Tools::Run::PiseApplication::clustalw.3 \
X		Bio::Tools::Run::PiseApplication::clustalw_convert.3 \
X		Bio::Tools::Run::PiseApplication::codcmp.3 \
X		Bio::Tools::Run::PiseApplication::coderet.3 \
X		Bio::Tools::Run::PiseApplication::codnocod.3 \
X		Bio::Tools::Run::PiseApplication::codontree.3 \
X		Bio::Tools::Run::PiseApplication::codonw.3 \
X		Bio::Tools::Run::PiseApplication::comalign.3 \
X		Bio::Tools::Run::PiseApplication::combat.3 \
X		Bio::Tools::Run::PiseApplication::compseq.3 \
X		Bio::Tools::Run::PiseApplication::con_filter.3 \
X		Bio::Tools::Run::PiseApplication::confmat.3 \
X		Bio::Tools::Run::PiseApplication::cons.3 \
X		Bio::Tools::Run::PiseApplication::consense.3 \
X		Bio::Tools::Run::PiseApplication::consensus.3 \
X		Bio::Tools::Run::PiseApplication::cpgplot.3 \
X		Bio::Tools::Run::PiseApplication::cpgreport.3 \
X		Bio::Tools::Run::PiseApplication::cusp.3 \
X		Bio::Tools::Run::PiseApplication::cutseq.3 \
X		Bio::Tools::Run::PiseApplication::dan.3 \
X		Bio::Tools::Run::PiseApplication::dca.3 \
X		Bio::Tools::Run::PiseApplication::decorate.3 \
X		Bio::Tools::Run::PiseApplication::degapseq.3 \
X		Bio::Tools::Run::PiseApplication::descseq.3 \
X		Bio::Tools::Run::PiseApplication::dialign2.3 \
X		Bio::Tools::Run::PiseApplication::diffseq.3 \
X		Bio::Tools::Run::PiseApplication::digest.3 \
X		Bio::Tools::Run::PiseApplication::distmat.3 \
X		Bio::Tools::Run::PiseApplication::distquart.3 \
X		Bio::Tools::Run::PiseApplication::dnadist.3 \
X		Bio::Tools::Run::PiseApplication::dnapars.3 \
X		Bio::Tools::Run::PiseApplication::dollop.3 \
X		Bio::Tools::Run::PiseApplication::domainer.3 \
X		Bio::Tools::Run::PiseApplication::dotmatcher.3 \
X		Bio::Tools::Run::PiseApplication::dotpath.3 \
X		Bio::Tools::Run::PiseApplication::dottup.3 \
X		Bio::Tools::Run::PiseApplication::drawgram.3 \
X		Bio::Tools::Run::PiseApplication::drawpyr.3 \
X		Bio::Tools::Run::PiseApplication::drawtree.3 \
X		Bio::Tools::Run::PiseApplication::dreg.3 \
X		Bio::Tools::Run::PiseApplication::druid.3 \
X		Bio::Tools::Run::PiseApplication::dsc.3 \
X		Bio::Tools::Run::PiseApplication::dssp.3 \
X		Bio::Tools::Run::PiseApplication::einverted.3 \
X		Bio::Tools::Run::PiseApplication::emma.3 \
X		Bio::Tools::Run::PiseApplication::emowse.3 \
X		Bio::Tools::Run::PiseApplication::environ.3 \
X		Bio::Tools::Run::PiseApplication::eprimer3.3 \
X		Bio::Tools::Run::PiseApplication::equicktandem.3 \
X		Bio::Tools::Run::PiseApplication::est2genome.3 \
X		Bio::Tools::Run::PiseApplication::etandem.3 \
X		Bio::Tools::Run::PiseApplication::extractfeat.3 \
X		Bio::Tools::Run::PiseApplication::extractseq.3 \
X		Bio::Tools::Run::PiseApplication::fasta.3 \
X		Bio::Tools::Run::PiseApplication::fastdnaml.3 \
X		Bio::Tools::Run::PiseApplication::fastrna.3 \
X		Bio::Tools::Run::PiseApplication::filtersites.3 \
X		Bio::Tools::Run::PiseApplication::findkm.3 \
X		Bio::Tools::Run::PiseApplication::fitch.3 \
X		Bio::Tools::Run::PiseApplication::fmtseq.3 \
X		Bio::Tools::Run::PiseApplication::freak.3 \
X		Bio::Tools::Run::PiseApplication::fuzznuc.3 \
X		Bio::Tools::Run::PiseApplication::fuzzpro.3 \
X		Bio::Tools::Run::PiseApplication::fuzztran.3 \
X		Bio::Tools::Run::PiseApplication::gb2xml.3 \
X		Bio::Tools::Run::PiseApplication::geecee.3 \
X		Bio::Tools::Run::PiseApplication::genscan.3 \
X		Bio::Tools::Run::PiseApplication::getblock.3 \
X		Bio::Tools::Run::PiseApplication::getorf.3 \
X		Bio::Tools::Run::PiseApplication::gff2ps.3 \
X		Bio::Tools::Run::PiseApplication::gibbs.3 \
X		Bio::Tools::Run::PiseApplication::gibbs_scan.3 \
X		Bio::Tools::Run::PiseApplication::golden.3 \
X		Bio::Tools::Run::PiseApplication::grailclnt.3 \
X		Bio::Tools::Run::PiseApplication::gruppi.3 \
X		Bio::Tools::Run::PiseApplication::helixturnhelix.3 \
X		Bio::Tools::Run::PiseApplication::hmmalign.3 \
X		Bio::Tools::Run::PiseApplication::hmmbuild.3 \
X		Bio::Tools::Run::PiseApplication::hmmcalibrate.3 \
X		Bio::Tools::Run::PiseApplication::hmmconvert.3 \
X		Bio::Tools::Run::PiseApplication::hmmemit.3 \
X		Bio::Tools::Run::PiseApplication::hmmer2sam.3 \
X		Bio::Tools::Run::PiseApplication::hmmfetch.3 \
X		Bio::Tools::Run::PiseApplication::hmmpfam.3 \
X		Bio::Tools::Run::PiseApplication::hmmscore.3 \
X		Bio::Tools::Run::PiseApplication::hmmsearch.3 \
X		Bio::Tools::Run::PiseApplication::hmoment.3 \
X		Bio::Tools::Run::PiseApplication::homology.3 \
X		Bio::Tools::Run::PiseApplication::html4blast.3 \
X		Bio::Tools::Run::PiseApplication::iep.3 \
X		Bio::Tools::Run::PiseApplication::infoalign.3 \
X		Bio::Tools::Run::PiseApplication::infoseq.3 \
X		Bio::Tools::Run::PiseApplication::interface.3 \
X		Bio::Tools::Run::PiseApplication::isochore.3 \
X		Bio::Tools::Run::PiseApplication::kitsch.3 \
X		Bio::Tools::Run::PiseApplication::lassap.3 \
X		Bio::Tools::Run::PiseApplication::lindna.3 \
X		Bio::Tools::Run::PiseApplication::listor.3 \
X		Bio::Tools::Run::PiseApplication::loadseq.3 \
X		Bio::Tools::Run::PiseApplication::lvb.3 \
X		Bio::Tools::Run::PiseApplication::makehist.3 \
X		Bio::Tools::Run::PiseApplication::map.3 \
X		Bio::Tools::Run::PiseApplication::marscan.3 \
X		Bio::Tools::Run::PiseApplication::maskfeat.3 \
X		Bio::Tools::Run::PiseApplication::maskseq.3 \
X		Bio::Tools::Run::PiseApplication::matcher.3 \
X		Bio::Tools::Run::PiseApplication::megamerger.3 \
X		Bio::Tools::Run::PiseApplication::melting.3 \
X		Bio::Tools::Run::PiseApplication::merger.3 \
X		Bio::Tools::Run::PiseApplication::mfold.3 \
X		Bio::Tools::Run::PiseApplication::mix.3 \
X		Bio::Tools::Run::PiseApplication::modelfromalign.3 \
X		Bio::Tools::Run::PiseApplication::most.3 \
X		Bio::Tools::Run::PiseApplication::mreps.3 \
X		Bio::Tools::Run::PiseApplication::msa.3 \
X		Bio::Tools::Run::PiseApplication::msbar.3 \
X		Bio::Tools::Run::PiseApplication::mspcrunch.3 \
X		Bio::Tools::Run::PiseApplication::mview_alig.3 \
X		Bio::Tools::Run::PiseApplication::mview_blast.3 \
X		Bio::Tools::Run::PiseApplication::mwfilter.3 \
X		Bio::Tools::Run::PiseApplication::needle.3 \
X		Bio::Tools::Run::PiseApplication::neighbor.3 \
X		Bio::Tools::Run::PiseApplication::newcpgreport.3 \
X		Bio::Tools::Run::PiseApplication::newcpgseek.3 \
X		Bio::Tools::Run::PiseApplication::newseq.3 \
X		Bio::Tools::Run::PiseApplication::njdist.3 \
X		Bio::Tools::Run::PiseApplication::nnssp.3 \
X		Bio::Tools::Run::PiseApplication::notseq.3 \
X		Bio::Tools::Run::PiseApplication::nrscope.3 \
X		Bio::Tools::Run::PiseApplication::nthseq.3 \
X		Bio::Tools::Run::PiseApplication::octanol.3 \
X		Bio::Tools::Run::PiseApplication::oddcomp.3 \
X		Bio::Tools::Run::PiseApplication::palindrome.3 \
X		Bio::Tools::Run::PiseApplication::pam.3 \
X		Bio::Tools::Run::PiseApplication::parciquart.3 \
X		Bio::Tools::Run::PiseApplication::pars.3 \
X		Bio::Tools::Run::PiseApplication::pasteseq.3 \
X		Bio::Tools::Run::PiseApplication::patmatdb.3 \
X		Bio::Tools::Run::PiseApplication::patmatmotifs.3 \
X		Bio::Tools::Run::PiseApplication::patser.3 \
X		Bio::Tools::Run::PiseApplication::pdbsearch.3 \
X		Bio::Tools::Run::PiseApplication::pepcoil.3 \
X		Bio::Tools::Run::PiseApplication::pepinfo.3 \
X		Bio::Tools::Run::PiseApplication::pepnet.3 \
X		Bio::Tools::Run::PiseApplication::pepstats.3 \
X		Bio::Tools::Run::PiseApplication::pepwheel.3 \
X		Bio::Tools::Run::PiseApplication::pepwindow.3 \
X		Bio::Tools::Run::PiseApplication::pepwindowall.3 \
X		Bio::Tools::Run::PiseApplication::pestfind.3 \
X		Bio::Tools::Run::PiseApplication::pftools.3 \
X		Bio::Tools::Run::PiseApplication::phiblast.3 \
X		Bio::Tools::Run::PiseApplication::pima.3 \
X		Bio::Tools::Run::PiseApplication::plotcon.3 \
X		Bio::Tools::Run::PiseApplication::plotorf.3 \
X		Bio::Tools::Run::PiseApplication::plsearch.3 \
X		Bio::Tools::Run::PiseApplication::polydot.3 \
X		Bio::Tools::Run::PiseApplication::pratt.3 \
X		Bio::Tools::Run::PiseApplication::predator.3 \
X		Bio::Tools::Run::PiseApplication::preg.3 \
X		Bio::Tools::Run::PiseApplication::prettyalign.3 \
X		Bio::Tools::Run::PiseApplication::prettyplot.3 \
X		Bio::Tools::Run::PiseApplication::prettyseq.3 \
X		Bio::Tools::Run::PiseApplication::primersearch.3 \
X		Bio::Tools::Run::PiseApplication::primo.3 \
X		Bio::Tools::Run::PiseApplication::prodom.3 \
X		Bio::Tools::Run::PiseApplication::profit.3 \
X		Bio::Tools::Run::PiseApplication::prophecy.3 \
X		Bio::Tools::Run::PiseApplication::prophet.3 \
X		Bio::Tools::Run::PiseApplication::prose.3 \
X		Bio::Tools::Run::PiseApplication::prot_nucml.3 \
X		Bio::Tools::Run::PiseApplication::protal2dna.3 \
X		Bio::Tools::Run::PiseApplication::protdist.3 \
X		Bio::Tools::Run::PiseApplication::protpars.3 \
X		Bio::Tools::Run::PiseApplication::pscan.3 \
X		Bio::Tools::Run::PiseApplication::psiblast.3 \
X		Bio::Tools::Run::PiseApplication::psort2.3 \
X		Bio::Tools::Run::PiseApplication::pyramids.3 \
X		Bio::Tools::Run::PiseApplication::pyreval.3 \
X		Bio::Tools::Run::PiseApplication::qstar.3 \
X		Bio::Tools::Run::PiseApplication::quicktree.3 \
X		Bio::Tools::Run::PiseApplication::readnexus.3 \
X		Bio::Tools::Run::PiseApplication::readseq.3 \
X		Bio::Tools::Run::PiseApplication::recoder.3 \
X		Bio::Tools::Run::PiseApplication::redata.3 \
X		Bio::Tools::Run::PiseApplication::remap.3 \
X		Bio::Tools::Run::PiseApplication::repeats.3 \
X		Bio::Tools::Run::PiseApplication::restover.3 \
X		Bio::Tools::Run::PiseApplication::restrict.3 \
X		Bio::Tools::Run::PiseApplication::revseq.3 \
X		Bio::Tools::Run::PiseApplication::rnadistance.3 \
X		Bio::Tools::Run::PiseApplication::rnaeval.3 \
X		Bio::Tools::Run::PiseApplication::rnafold.3 \
X		Bio::Tools::Run::PiseApplication::rnaga.3 \
X		Bio::Tools::Run::PiseApplication::rnaheat.3 \
X		Bio::Tools::Run::PiseApplication::rnainverse.3 \
X		Bio::Tools::Run::PiseApplication::rnapdist.3 \
X		Bio::Tools::Run::PiseApplication::rnasubopt.3 \
X		Bio::Tools::Run::PiseApplication::sam2hmmer.3 \
X		Bio::Tools::Run::PiseApplication::sampleseqs.3 \
X		Bio::Tools::Run::PiseApplication::saps.3 \
X		Bio::Tools::Run::PiseApplication::satellites.3 \
X		Bio::Tools::Run::PiseApplication::scan_for_matches.3 \
X		Bio::Tools::Run::PiseApplication::scope.3 \
X		Bio::Tools::Run::PiseApplication::scopparse.3 \
X		Bio::Tools::Run::PiseApplication::seqboot.3 \
X		Bio::Tools::Run::PiseApplication::seqgen.3 \
X		Bio::Tools::Run::PiseApplication::seqmatchall.3 \
X		Bio::Tools::Run::PiseApplication::seqsblast.3 \
X		Bio::Tools::Run::PiseApplication::seqstat.3 \
X		Bio::Tools::Run::PiseApplication::showalign.3 \
X		Bio::Tools::Run::PiseApplication::showfeat.3 \
X		Bio::Tools::Run::PiseApplication::showorf.3 \
X		Bio::Tools::Run::PiseApplication::showseq.3 \
X		Bio::Tools::Run::PiseApplication::shuffleseq.3 \
X		Bio::Tools::Run::PiseApplication::sigcleave.3 \
X		Bio::Tools::Run::PiseApplication::siggen.3 \
X		Bio::Tools::Run::PiseApplication::sigscan.3 \
X		Bio::Tools::Run::PiseApplication::silent.3 \
X		Bio::Tools::Run::PiseApplication::sirna.3 \
X		Bio::Tools::Run::PiseApplication::splitter.3 \
X		Bio::Tools::Run::PiseApplication::sreformat.3 \
X		Bio::Tools::Run::PiseApplication::stretcher.3 \
X		Bio::Tools::Run::PiseApplication::stride.3 \
X		Bio::Tools::Run::PiseApplication::stssearch.3 \
X		Bio::Tools::Run::PiseApplication::supermatcher.3 \
X		Bio::Tools::Run::PiseApplication::syco.3 \
X		Bio::Tools::Run::PiseApplication::tacg.3 \
X		Bio::Tools::Run::PiseApplication::tfscan.3 \
X		Bio::Tools::Run::PiseApplication::tipdate.3 \
X		Bio::Tools::Run::PiseApplication::tmap.3 \
X		Bio::Tools::Run::PiseApplication::toppred.3 \
X		Bio::Tools::Run::PiseApplication::tranalign.3 \
X		Bio::Tools::Run::PiseApplication::transeq.3 \
X		Bio::Tools::Run::PiseApplication::treealign.3 \
X		Bio::Tools::Run::PiseApplication::trimest.3 \
X		Bio::Tools::Run::PiseApplication::trimseq.3 \
X		Bio::Tools::Run::PiseApplication::trnascan.3 \
X		Bio::Tools::Run::PiseApplication::twofeat.3 \
X		Bio::Tools::Run::PiseApplication::unroot.3 \
X		Bio::Tools::Run::PiseApplication::vectorstrip.3 \
X		Bio::Tools::Run::PiseApplication::water.3 \
X		Bio::Tools::Run::PiseApplication::weighbor.3 \
X		Bio::Tools::Run::PiseApplication::whichdb.3 \
X		Bio::Tools::Run::PiseApplication::wise2.3 \
X		Bio::Tools::Run::PiseApplication::wobble.3 \
X		Bio::Tools::Run::PiseApplication::wordcount.3 \
X		Bio::Tools::Run::PiseApplication::wordmatch.3 \
X		Bio::Tools::Run::PiseApplication::wublast2.3 \
X		Bio::Tools::Run::PiseApplication::xblast.3 \
X		Bio::Tools::Run::PiseApplication::xpound.3 \
X		Bio::Tools::Run::PiseJob.3 \
X		Bio::Tools::Run::PiseJobParser.3 \
X		Bio::Tools::Run::PiseWorkflow.3 \
X		Bio::Tools::Run::Primate.3 \
X		Bio::Tools::Run::Primer3.3 \
X		Bio::Tools::Run::Prints.3 \
X		Bio::Tools::Run::Profile.3 \
X		Bio::Tools::Run::Promoterwise.3 \
X		Bio::Tools::Run::Pseudowise.3 \
X		Bio::Tools::Run::RepeatMasker.3 \
X		Bio::Tools::Run::Seg.3 \
X		Bio::Tools::Run::Signalp.3 \
X		Bio::Tools::Run::Tmhmm.3 \
X		Bio::Tools::Run::TribeMCL.3 \
X		Bio::Tools::Run::Vista.3
X
X.include <bsd.port.pre.mk>
X
X.if ${PERL_LEVEL} < 500600
XIGNORE=		requires Perl 5.6 or better
X.endif
X
X# now install all extra stuff (docs, examples, scripts)
Xpost-install:
X	${MKDIR} ${DATADIR}
X	${CP} -R ${WRKSRC}/scripts ${DATADIR}
X	${MKDIR} ${EXAMPLESDIR}
X	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
X.if !defined(NOPORTDOCS)
X	${MKDIR} ${DOCSDIR}
X.for doc in AUTHORS Changes INSTALL.PROGRAMS README
X	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
X.endfor
X.endif
X
X.include <bsd.port.post.mk>
END-of-biology/p5-bioperl-run-devel/Makefile
exit


>Release-Note:
>Audit-Trail:
>Unformatted:



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