Date: Mon, 6 Mar 2006 03:32:16 GMT From: Mauricio Herrera Cuadra <mauricio@arareko.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/94123: [maintainer update] Update port: biology/ruby-bio to version 1.0.0 Message-ID: <200603060332.k263WG3k049269@www.freebsd.org> Resent-Message-ID: <200603060340.k263e4DN056529@freefall.freebsd.org>
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>Number: 94123 >Category: ports >Synopsis: [maintainer update] Update port: biology/ruby-bio to version 1.0.0 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Mon Mar 06 03:40:04 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: Thu Mar 2 10:07:06 CST 2006 root@nordwand.arareko.net:/usr/obj/usr/src/sys/nordwand i386 >Description: This patch updates the biology/ruby-bio port to its 1.0.0 version. I'll maintain this port. >How-To-Repeat: >Fix: diff -ruN biology/ruby-bio.old/Makefile biology/ruby-bio/Makefile --- biology/ruby-bio.old/Makefile Sun Mar 5 22:05:34 2006 +++ biology/ruby-bio/Makefile Sun Mar 5 22:07:24 2006 @@ -6,23 +6,44 @@ # PORTNAME= bio -PORTVERSION= 0.6.2 +PORTVERSION= 1.0.0 CATEGORIES= biology ruby MASTER_SITES= http://bioruby.org/archive/ PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX} DISTNAME= ${PORTNAME}ruby-${PORTVERSION} DIST_SUBDIR= ruby -MAINTAINER= ports@FreeBSD.org +MAINTAINER= mauricio@arareko.net COMMENT= Integrated environment for Bioinformatics written in Ruby +OPTIONS= XMLPARSER "xmlparser support for faster Blast processing" off \ + BDB4 "bdb4 support for faster flat file indexing" off \ + MYSQL "MySQL database support for BioSQL" off \ + PGSQL "PostgreSQL database support for BioSQL" off +OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNAME}/options + USE_RUBY= yes USE_RUBY_SETUP= yes RUBY_SETUP= install.rb +.include <bsd.port.pre.mk> + +.if defined(WITH_XMLPARSER) +RUN_DEPENDS+= ${RUBY_SITEARCHLIBDIR}/xmlparser.so:${PORTSDIR}/textproc/ruby-xmlparser +.endif +.if defined(WITH_BDB4) +RUN_DEPENDS+= ${RUBY_SITEARCHLIBDIR}/bdb.so:${PORTSDIR}/databases/ruby-bdb +.endif +.if defined(WITH_MYSQL) +RUN_DEPENDS+= ${RUBY_SITELIBDIR}/DBD/Mysql/Mysql.rb:${PORTSDIR}/databases/ruby-dbd_mysql +.endif +.if defined(WITH_PGSQL) +RUN_DEPENDS+= ${RUBY_SITELIBDIR}/DBD/Pg/Pg.rb:${PORTSDIR}/databases/ruby-dbd_pg +.endif + post-patch: ${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \ - ${WRKSRC}/doc/Tutorial.rd.ja \ + ${WRKSRC}/doc/Tutorial.rd \ ${WRKSRC}/lib/bio/io/registry.rb do-install: @@ -38,7 +59,8 @@ ${CP} -R ${WRKSRC}/sample/ ${RUBY_MODEXAMPLESDIR}/ ${MKDIR} ${RUBY_MODDOCDIR}/ja ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README ${RUBY_MODDOCDIR}/ - ${INSTALL_DATA} ${WRKSRC}/doc/*.ja ${RUBY_MODDOCDIR}/ja/ + ${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${RUBY_MODDOCDIR}/ + ${INSTALL_DATA} ${WRKSRC}/doc/*.rd.ja ${RUBY_MODDOCDIR}/ja/ .endif -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff -ruN biology/ruby-bio.old/distinfo biology/ruby-bio/distinfo --- biology/ruby-bio.old/distinfo Sun Mar 5 22:05:34 2006 +++ biology/ruby-bio/distinfo Sun Mar 5 22:07:24 2006 @@ -1,3 +1,3 @@ -MD5 (ruby/bioruby-0.6.2.tar.gz) = 68c7ae5aa8562bfe1021d9a5201a9581 -SHA256 (ruby/bioruby-0.6.2.tar.gz) = 92400eab772f1b1f2943adaa5f2915e0c2c1abc559d486c83780aa62f4d903b5 -SIZE (ruby/bioruby-0.6.2.tar.gz) = 270444 +MD5 (ruby/bioruby-1.0.0.tar.gz) = 5106b71b9b53bce7c3b93df911d2411d +SHA256 (ruby/bioruby-1.0.0.tar.gz) = 7d4255e0a032ef21acea32eb1b3051843b3363008f7a36d7515430e2823b1be3 +SIZE (ruby/bioruby-1.0.0.tar.gz) = 573771 diff -ruN biology/ruby-bio.old/pkg-plist biology/ruby-bio/pkg-plist --- biology/ruby-bio.old/pkg-plist Sun Mar 5 22:05:34 2006 +++ biology/ruby-bio/pkg-plist Sun Mar 5 22:07:24 2006 @@ -1,3 +1,4 @@ +bin/bioruby bin/br_biofetch.rb bin/br_bioflat.rb bin/br_biogetseq.rb @@ -8,8 +9,23 @@ @dirrm etc/bioinformatics %%RUBY_SITELIBDIR%%/bio.rb %%RUBY_SITELIBDIR%%/bio/alignment.rb -%%RUBY_SITELIBDIR%%/bio/appl/alignfactory.rb +%%RUBY_SITELIBDIR%%/bio/command.rb +%%RUBY_SITELIBDIR%%/bio/db.rb +%%RUBY_SITELIBDIR%%/bio/feature.rb +%%RUBY_SITELIBDIR%%/bio/location.rb +%%RUBY_SITELIBDIR%%/bio/pathway.rb +%%RUBY_SITELIBDIR%%/bio/reference.rb +%%RUBY_SITELIBDIR%%/bio/sequence.rb +%%RUBY_SITELIBDIR%%/bio/shell.rb %%RUBY_SITELIBDIR%%/bio/appl/blast.rb +%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb +%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb +%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb +%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb +%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb +%%RUBY_SITELIBDIR%%/bio/appl/psort.rb +%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb +%%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/report.rb @@ -17,20 +33,13 @@ %%RUBY_SITELIBDIR%%/bio/appl/blast/wublast.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb %%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb -%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb %%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb -%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb -%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb %%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb %%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb %%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb -%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb %%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb -%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb %%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb -%%RUBY_SITELIBDIR%%/bio/appl/psort.rb %%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb -%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb %%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb %%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb %%RUBY_SITELIBDIR%%/bio/appl/spidey/report.rb @@ -39,67 +48,163 @@ %%RUBY_SITELIBDIR%%/bio/data/aa.rb %%RUBY_SITELIBDIR%%/bio/data/codontable.rb %%RUBY_SITELIBDIR%%/bio/data/na.rb -%%RUBY_SITELIBDIR%%/bio/db.rb %%RUBY_SITELIBDIR%%/bio/db/aaindex.rb -%%RUBY_SITELIBDIR%%/bio/db/embl.rb +%%RUBY_SITELIBDIR%%/bio/db/fantom.rb +%%RUBY_SITELIBDIR%%/bio/db/fasta.rb +%%RUBY_SITELIBDIR%%/bio/db/gff.rb +%%RUBY_SITELIBDIR%%/bio/db/go.rb +%%RUBY_SITELIBDIR%%/bio/db/litdb.rb +%%RUBY_SITELIBDIR%%/bio/db/medline.rb +%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb +%%RUBY_SITELIBDIR%%/bio/db/pdb.rb +%%RUBY_SITELIBDIR%%/bio/db/prosite.rb +%%RUBY_SITELIBDIR%%/bio/db/rebase.rb +%%RUBY_SITELIBDIR%%/bio/db/transfac.rb %%RUBY_SITELIBDIR%%/bio/db/embl/common.rb %%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb %%RUBY_SITELIBDIR%%/bio/db/embl/sptr.rb %%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb %%RUBY_SITELIBDIR%%/bio/db/embl/trembl.rb -%%RUBY_SITELIBDIR%%/bio/db/fantom.rb -%%RUBY_SITELIBDIR%%/bio/db/fasta.rb -%%RUBY_SITELIBDIR%%/bio/db/genbank.rb +%%RUBY_SITELIBDIR%%/bio/db/embl/uniprot.rb %%RUBY_SITELIBDIR%%/bio/db/genbank/common.rb %%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb %%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb %%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb %%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb -%%RUBY_SITELIBDIR%%/bio/db/gff.rb -%%RUBY_SITELIBDIR%%/bio/db/go.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb +%%RUBY_SITELIBDIR%%/bio/db/kegg/expression.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/genome.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/glycan.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb +%%RUBY_SITELIBDIR%%/bio/db/kegg/kgml.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/ko.rb -%%RUBY_SITELIBDIR%%/bio/db/kegg/microarray.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb -%%RUBY_SITELIBDIR%%/bio/db/litdb.rb -%%RUBY_SITELIBDIR%%/bio/db/medline.rb -%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb -%%RUBY_SITELIBDIR%%/bio/db/pdb.rb %%RUBY_SITELIBDIR%%/bio/db/pdb/atom.rb %%RUBY_SITELIBDIR%%/bio/db/pdb/chain.rb +%%RUBY_SITELIBDIR%%/bio/db/pdb/chemicalcomponent.rb %%RUBY_SITELIBDIR%%/bio/db/pdb/model.rb %%RUBY_SITELIBDIR%%/bio/db/pdb/pdb.rb %%RUBY_SITELIBDIR%%/bio/db/pdb/residue.rb %%RUBY_SITELIBDIR%%/bio/db/pdb/utils.rb -%%RUBY_SITELIBDIR%%/bio/db/prosite.rb -%%RUBY_SITELIBDIR%%/bio/db/transfac.rb -%%RUBY_SITELIBDIR%%/bio/extend.rb -%%RUBY_SITELIBDIR%%/bio/feature.rb -%%RUBY_SITELIBDIR%%/bio/io/brdb.rb %%RUBY_SITELIBDIR%%/bio/io/das.rb %%RUBY_SITELIBDIR%%/bio/io/dbget.rb %%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb +%%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb %%RUBY_SITELIBDIR%%/bio/io/fetch.rb %%RUBY_SITELIBDIR%%/bio/io/flatfile.rb -%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb -%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb -%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb +%%RUBY_SITELIBDIR%%/bio/io/higet.rb %%RUBY_SITELIBDIR%%/bio/io/keggapi.rb %%RUBY_SITELIBDIR%%/bio/io/pubmed.rb %%RUBY_SITELIBDIR%%/bio/io/registry.rb %%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb %%RUBY_SITELIBDIR%%/bio/io/sql.rb -%%RUBY_SITELIBDIR%%/bio/location.rb -%%RUBY_SITELIBDIR%%/bio/pathway.rb -%%RUBY_SITELIBDIR%%/bio/reference.rb -%%RUBY_SITELIBDIR%%/bio/sequence.rb +%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb +%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb +%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb +%%RUBY_SITELIBDIR%%/bio/sequence/aa.rb +%%RUBY_SITELIBDIR%%/bio/sequence/common.rb +%%RUBY_SITELIBDIR%%/bio/sequence/compat.rb +%%RUBY_SITELIBDIR%%/bio/sequence/format.rb +%%RUBY_SITELIBDIR%%/bio/sequence/generic.rb +%%RUBY_SITELIBDIR%%/bio/sequence/na.rb +%%RUBY_SITELIBDIR%%/bio/shell/core.rb +%%RUBY_SITELIBDIR%%/bio/shell/demo.rb +%%RUBY_SITELIBDIR%%/bio/shell/interface.rb +%%RUBY_SITELIBDIR%%/bio/shell/object.rb +%%RUBY_SITELIBDIR%%/bio/shell/web.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/codon.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/emboss.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/entry.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/flatfile.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/keggapi.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/midi.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/obda.rb +%%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/Rakefile +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers/application.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers/shell_controller.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/helpers/application_helper.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/models/shell_connection.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/layouts/shell.rhtml +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/history.rhtml +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/index.rhtml +%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/show.rhtml +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/boot.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/database.yml +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environment.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/routes.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/development.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/production.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/test.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/doc/README_FOR_APP +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/404.html +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/500.html +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.cgi +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.fcgi +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.rb +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/favicon.ico +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/index.html +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/robots.txt +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/images/icon.png +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/images/rails.png +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/controls.js +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/dragdrop.js +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/effects.js +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/prototype.js +%%RUBY_SITELIBDIR%%/bio/shell/rails/public/stylesheets/main.css +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/about +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/breakpointer +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/console +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/destroy +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/generate +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/plugin +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/runner +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/server +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance/benchmarker +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance/profiler +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/reaper +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/spawner +%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/spinner +%%RUBY_SITELIBDIR%%/bio/shell/rails/test/test_helper.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb +%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb +%%RUBY_SITELIBDIR%%/bio/util/sirna.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/buried.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/helix.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/hydropathy.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/nucleotide.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/strand.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/taylor.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/turn.rb +%%RUBY_SITELIBDIR%%/bio/util/color_scheme/zappo.rb +@dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme +@dirrm %%RUBY_SITELIBDIR%%/bio/util +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/test +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script/process +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/stylesheets +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/images +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/doc +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/config +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/layouts +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/models +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/helpers +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails +@dirrm %%RUBY_SITELIBDIR%%/bio/shell/plugin +@dirrm %%RUBY_SITELIBDIR%%/bio/shell +@dirrm %%RUBY_SITELIBDIR%%/bio/sequence @dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile @dirrm %%RUBY_SITELIBDIR%%/bio/io @dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb @@ -121,9 +226,12 @@ @dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw @dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat @dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast +@dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq @dirrm %%RUBY_SITELIBDIR%%/bio/appl @dirrm %%RUBY_SITELIBDIR%%/bio +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/any2fasta.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb @@ -139,6 +247,7 @@ %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gt2fasta.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmfetch.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmsearch.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/psortplot_html.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/ssearch2tab.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tdiary.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tfastx2tab.rb @@ -146,6 +255,9 @@ %%PORTDOCS%%@dirrm %%RUBY_MODEXAMPLESDIR%% %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ChangeLog %%PORTDOCS%%%%RUBY_MODDOCDIR%%/README +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/KEGG_API.rd +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Tutorial.rd +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-0.7.rd %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/BioRuby.rd.ja %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Design.rd.ja %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja >Release-Note: >Audit-Trail: >Unformatted:
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