ports/132122: [Update]biology/p5-bioperl-run:update to 1.6.1
Wen Heping
wenheping at gmail.com
Thu Feb 26 11:20:02 UTC 2009
>Number: 132122
>Category: ports
>Synopsis: [Update]biology/p5-bioperl-run:update to 1.6.1
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Thu Feb 26 11:20:01 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator: Wen Heping
>Release: FreeBSD 8.0-CURRENT
>Organization:
ChangAn Middle School
>Environment:
FreeBSD fb8.wenjing.com 8.0-CURRENT-200811 FreeBSD 8.0-CURRENT-200811 #0: Thu Nov 6 00:32:12 UTC 2008 root at almeida.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC i386
>Description:
update to 1.6.1 from 1.4
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
--- Makefile.orig 2009-02-25 21:09:07.000000000 +0800
+++ Makefile 2009-02-26 18:42:07.000000000 +0800
@@ -6,362 +6,133 @@
#
PORTNAME= bioperl-run
-PORTVERSION= 1.4
-PORTREVISION= 1
+PORTVERSION= 1.6.1
CATEGORIES= biology perl5
MASTER_SITES= http://bioperl.org/DIST/ \
CPAN
PKGNAMEPREFIX= p5-
+DISTNAME= BioPerl-run-${PORTVERSION}
MAINTAINER= mauricio at arareko.net
COMMENT= Wrapper modules for common bioinformatics tools
-BUILD_DEPENDS= p5-bioperl=1.4_2:${PORTSDIR}/biology/p5-bioperl \
+BUILD_DEPENDS= p5-bioperl=1.6.0:${PORTSDIR}/biology/p5-bioperl \
+ ${SITE_PERL}/IPC/Run.pm:${PORTSDIR}/devel/p5-IPC-Run \
${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
RUN_DEPENDS= ${BUILD_DEPENDS}
CONFLICTS= p5-bioperl-run-1.[13579]*
-PERL_CONFIGURE= YES
+PERL_MODBUILD= YES
+WRKSRC= ${WRKDIR}/BioPerl-run-1.6.0
-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 \
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- 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 \
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+ bp_multi_hmmsearch.pl.1 \
+ bp_panalysis.pl.1 \
+ bp_papplmaker.pl.1 \
+ bp_run_neighbor.pl.1 \
+ bp_run_protdist.pl.1
+
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+ 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}
- ${MKDIR} ${EXAMPLESDIR}
- @${CP} -Rv ${WRKSRC}/examples/* ${EXAMPLESDIR}
.if !defined(NOPORTDOCS)
${MKDIR} ${DOCSDIR}
.for doc in AUTHORS Changes INSTALL.PROGRAMS README
--- distinfo.orig 2009-02-25 21:09:07.000000000 +0800
+++ distinfo 2009-02-26 06:09:01.000000000 +0800
@@ -1,3 +1,3 @@
-MD5 (bioperl-run-1.4.tar.gz) = 25914ab48d1ab0393ebb067a8f68a821
-SHA256 (bioperl-run-1.4.tar.gz) = 54eea327c8f80061d6c45e56b64d5c51daa20b723390eed1a3377f3a61645d86
-SIZE (bioperl-run-1.4.tar.gz) = 830774
+MD5 (BioPerl-run-1.6.1.tar.gz) = 15f53f5232b9ed58fa27662431935da8
+SHA256 (BioPerl-run-1.6.1.tar.gz) = 1ecf2f3a0dd606a1522642d6dd05f8641cd5c8788f3b53e19243f4121c4d4b80
+SIZE (BioPerl-run-1.6.1.tar.gz) = 4082463
--- pkg-plist.orig 2009-02-25 21:09:07.000000000 +0800
+++ pkg-plist 2009-02-26 18:41:58.000000000 +0800
@@ -1,366 +1,128 @@
+bin/bp_papplmaker.pl
+bin/bp_panalysis.pl
+bin/bp_run_neighbor.pl
+bin/bp_multi_hmmsearch.pl
+bin/bp_bioperl_application_installer.pl
+bin/bp_run_protdist.pl
+%%PORTDATA%%%%DATADIR%%/scripts/bioperl_application_installer.PLS
+%%PORTDATA%%%%DATADIR%%/scripts/multi_hmmsearch.PLS
+%%PORTDATA%%%%DATADIR%%/scripts/panalysis.PLS
+%%PORTDATA%%%%DATADIR%%/scripts/papplmaker.PLS
+%%PORTDATA%%%%DATADIR%%/scripts/run_neighbor.PLS
+%%PORTDATA%%%%DATADIR%%/scripts/run_protdist.PLS
+%%PORTDATA%%@dirrm %%DATADIR%%/scripts
+%%PORTDATA%%@dirrm %%DATADIR%%
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/
%%SITE_PERL%%/Bio/Factory/EMBOSS.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm
%%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
%%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probalign.pm
%%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Pal2Nal.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probcons.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Kalign.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm
%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm
-%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm
%%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/Pise.pm
%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/Coil.pm
-%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
-%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
-%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
-%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
-%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
-%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
-%%SITE_PERL%%/Bio/Tools/Run/Hmmpfam.pm
-%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/REL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
%%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree/Best.pm
%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Codeml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Baseml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Evolver.pm
%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Yn00.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/CSR.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/Puzzle.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/abiview.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/addquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/align2model.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/alistat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/antigenic.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/assp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/backtranseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bambe.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/banana.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bionj.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/biosed.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bl2seq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blast2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps_block.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps_matrix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/boxshade.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/btwisted.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cai.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cds.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/chaos.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/charge.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/checktrans.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/chips.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cirdna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clique.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clustalw.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clustalw_convert.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codcmp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/coderet.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codnocod.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codontree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codonw.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/comalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/combat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/compseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/con_filter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/confmat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cons.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/consense.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/consensus.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cpgplot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cpgreport.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cusp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cutseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dca.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/decorate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/degapseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/descseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dialign2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/diffseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/digest.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/distmat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/distquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dnadist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dnapars.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dollop.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/domainer.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dotmatcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dotpath.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dottup.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawgram.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawpyr.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawtree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dreg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/druid.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dsc.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dssp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/einverted.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/emma.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/emowse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/environ.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/eprimer3.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/est2genome.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/etandem.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/extractfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/extractseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fasta.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fastdnaml.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fastrna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/filtersites.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/findkm.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fitch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fmtseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/freak.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzznuc.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzzpro.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzztran.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gb2xml.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/getblock.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/getorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gff2ps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gibbs.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/grailclnt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gruppi.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/helixturnhelix.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmbuild.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmcalibrate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmconvert.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmemit.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmer2sam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmfetch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmpfam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmscore.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmoment.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/homology.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/html4blast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/iep.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/infoalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/infoseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/interface.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/isochore.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/kitsch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lassap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lgicsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lindna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/listor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/loadseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lvb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/makehist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/map.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newcpgseek.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/njdist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nnssp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/notseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nrscope.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nthseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/octanol.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/oddcomp.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patmatmotifs.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwheel.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plotorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plsearch.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pratt.pm
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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/readseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/recoder.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/redata.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/remap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/repeats.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/restover.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/restrict.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/revseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnadistance.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnaeval.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnafold.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnaga.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnaheat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnainverse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnapdist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnasubopt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sam2hmmer.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sampleseqs.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/saps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/satellites.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/scan_for_matches.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/scope.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/scopparse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqboot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqgen.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqmatchall.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqsblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqstat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/shuffleseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigcleave.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/siggen.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/silent.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sirna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/splitter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sreformat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stretcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stride.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stssearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/supermatcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/syco.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tacg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tfscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tipdate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tmap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/toppred.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tranalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/transeq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/treealign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimest.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trnascan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/twofeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/unroot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/vectorstrip.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/water.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/weighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/whichdb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wise2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wobble.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordcount.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordmatch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wublast2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xpound.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseJob.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseJobParser.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseWorkflow.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PhyloBase.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/SLR.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Semphy.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
+%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
+%%SITE_PERL%%/Bio/Tools/Run/ERPIN.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
+%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
+%%SITE_PERL%%/Bio/Tools/Run/Match.pm
%%SITE_PERL%%/Bio/Tools/Run/Primate.pm
-%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
+%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
+%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
+%%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
+%%SITE_PERL%%/Bio/Tools/Run/Simprot.pm
+%%SITE_PERL%%/Bio/Tools/Run/MCS.pm
+%%SITE_PERL%%/Bio/Tools/Run/Coil.pm
+%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
%%SITE_PERL%%/Bio/Tools/Run/Prints.pm
-%%SITE_PERL%%/Bio/Tools/Run/Profile.pm
+%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
+%%SITE_PERL%%/Bio/Tools/Run/Vista.pm
+%%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm
+%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
+%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
%%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm
-%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
-%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
-%%SITE_PERL%%/Bio/Tools/Run/Seg.pm
+%%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm
+%%SITE_PERL%%/Bio/Tools/Run/Cap3.pm
+%%SITE_PERL%%/Bio/Tools/Run/Glimmer.pm
+%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
%%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
+%%SITE_PERL%%/Bio/Tools/Run/Meme.pm
+%%SITE_PERL%%/Bio/Tools/Run/RNAMotif.pm
+%%SITE_PERL%%/Bio/Tools/Run/Seg.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genemark.pm
+%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
+%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
+%%SITE_PERL%%/Bio/Tools/Run/Profile.pm
%%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
-%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
-%%SITE_PERL%%/Bio/Tools/Run/Vista.pm
-%%DATADIR%%/scripts/panalysis.PLS
-%%DATADIR%%/scripts/papplmaker.PLS
-%%DATADIR%%/scripts/run_neighbor.PLS
-%%DATADIR%%/scripts/run_protdist.PLS
-%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
-%%PORTDOCS%%%%DOCSDIR%%/Changes
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%EXAMPLESDIR%%/pise/blast-kun.pl
-%%EXAMPLESDIR%%/pise/blast2.pl
-%%EXAMPLESDIR%%/pise/clustalw.pl
-%%EXAMPLESDIR%%/pise/dnadist.data
-%%EXAMPLESDIR%%/pise/dnadist.pl
-%%EXAMPLESDIR%%/pise/genscan.pl
-%%EXAMPLESDIR%%/pise/needle.pl
-%%EXAMPLESDIR%%/pise/phylo-kun.pl
-%%EXAMPLESDIR%%/pise/toppred.pl
- at dirrm %%EXAMPLESDIR%%/pise
- at dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
- at dirrm %%DATADIR%%/scripts
- at dirrm %%DATADIR%%
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/PiseApplication
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
+%%SITE_PERL%%/Bio/Tools/Run/Ensembl.pm
+%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
+%%SITE_PERL%%/Bio/Installer/EMBOSS.pm
+%%SITE_PERL%%/Bio/Installer/Muscle.pm
+%%SITE_PERL%%/Bio/Installer/Clustalw.pm
+%%SITE_PERL%%/Bio/Installer/SLR.pm
+%%SITE_PERL%%/Bio/Installer/Probcons.pm
+%%SITE_PERL%%/Bio/Installer/TCoffee.pm
+%%SITE_PERL%%/Bio/Installer/Hyphy.pm
+%%SITE_PERL%%/Bio/Installer/Generic.pm
+%%SITE_PERL%%/Bio/Installer/PAML.pm
+ at dirrm %%SITE_PERL%%/Bio/Installer
@dirrm %%SITE_PERL%%/Bio/Tools/Run/Analysis
@dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
+ at dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo
@dirrmtry %%SITE_PERL%%/Bio/Tools/Run
@dirrmtry %%SITE_PERL%%/Bio/Tools
- at dirrmtry %%SITE_PERL%%/Bio/Factory
@dirrmtry %%SITE_PERL%%/Bio
>Release-Note:
>Audit-Trail:
>Unformatted:
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