From nobody@FreeBSD.org Tue Feb 21 19:46:13 2006 Return-Path: Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 09F0216A420 for ; Tue, 21 Feb 2006 19:46:13 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [216.136.204.117]) by mx1.FreeBSD.org (Postfix) with ESMTP id BDB0443D46 for ; Tue, 21 Feb 2006 19:46:12 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.13.1/8.13.1) with ESMTP id k1LJkCPw014387 for ; Tue, 21 Feb 2006 19:46:12 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.13.1/8.13.1/Submit) id k1LJkC7a014386; Tue, 21 Feb 2006 19:46:12 GMT (envelope-from nobody) Message-Id: <200602211946.k1LJkC7a014386@www.freebsd.org> Date: Tue, 21 Feb 2006 19:46:12 GMT From: Mauricio Herrera Cuadra To: freebsd-gnats-submit@FreeBSD.org Subject: New port: biology/p5-bioperl-run Wrapper modules for common bioinformatics tools X-Send-Pr-Version: www-2.3 >Number: 93674 >Category: ports >Synopsis: New port: biology/p5-bioperl-run Wrapper modules for common bioinformatics tools >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: closed >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Feb 21 19:50:02 GMT 2006 >Closed-Date: Tue May 02 21:33:28 GMT 2006 >Last-Modified: Tue May 02 21:33:28 GMT 2006 >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 1.4 release 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 # biology/p5-bioperl-run/pkg-plist # biology/p5-bioperl-run/pkg-descr # biology/p5-bioperl-run/distinfo # biology/p5-bioperl-run/Makefile # echo c - biology/p5-bioperl-run mkdir -p biology/p5-bioperl-run > /dev/null 2>&1 echo x - biology/p5-bioperl-run/pkg-plist sed 's/^X//' >biology/p5-bioperl-run/pkg-plist << 'END-of-biology/p5-bioperl-run/pkg-plist' X%%SITE_PERL%%/Bio/Factory/EMBOSS.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm X%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm X%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm X%%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm 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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/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 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@dirrmtry %%SITE_PERL%%/Bio/Factory X@dirrmtry %%SITE_PERL%%/Bio END-of-biology/p5-bioperl-run/pkg-plist echo x - biology/p5-bioperl-run/pkg-descr sed 's/^X//' >biology/p5-bioperl-run/pkg-descr << 'END-of-biology/p5-bioperl-run/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/pkg-descr echo x - biology/p5-bioperl-run/distinfo sed 's/^X//' >biology/p5-bioperl-run/distinfo << 'END-of-biology/p5-bioperl-run/distinfo' XMD5 (bioperl-run-1.4.tar.gz) = 25914ab48d1ab0393ebb067a8f68a821 XSHA256 (bioperl-run-1.4.tar.gz) = 54eea327c8f80061d6c45e56b64d5c51daa20b723390eed1a3377f3a61645d86 XSIZE (bioperl-run-1.4.tar.gz) = 830774 END-of-biology/p5-bioperl-run/distinfo echo x - biology/p5-bioperl-run/Makefile sed 's/^X//' >biology/p5-bioperl-run/Makefile << 'END-of-biology/p5-bioperl-run/Makefile' X# New ports collection makefile for: biology/p5-bioperl-run X# Date created: 21 February 2006 X# Whom: Mauricio Herrera Cuadra X# X# $FreeBSD$ X# X XPORTNAME= bioperl-run XPORTVERSION= 1.4 XCATEGORIES= biology perl5 XMASTER_SITES= http://bioperl.org/DIST/ \ X ${MASTER_SITE_PERL_CPAN} XPKGNAMEPREFIX= p5- X XMAINTAINER= mauricio@arareko.net XCOMMENT= Wrapper modules for common bioinformatics tools X XBUILD_DEPENDS= p5-bioperl=1.4:${PORTSDIR}/biology/p5-bioperl \ X ${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff XRUN_DEPENDS= ${BUILD_DEPENDS} X XCONFLICTS= p5-bioperl-run-1.[13579]* X XPERL_CONFIGURE= YES X XMAN3= Bio::Factory::EMBOSS.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::Lagan.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::Hmmpfam.3 \ X Bio::Tools::Run::Mdust.3 \ X Bio::Tools::Run::Phylo::Molphy::ProtML.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 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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 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 END-of-biology/p5-bioperl-run/Makefile exit >Release-Note: >Audit-Trail: State-Changed-From-To: open->closed State-Changed-By: garga State-Changed-When: Tue May 2 21:33:26 UTC 2006 State-Changed-Why: New port added. Thanks! http://www.freebsd.org/cgi/query-pr.cgi?pr=93674 >Unformatted: