Attachment 63057 Details for Bug 94123 – file.diff

[patch] file.diff

file.diff (text/plain), 14.97 KB, created by Mauricio Herrera Cuadra on 2006-03-06 03:40:04 UTC

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Filename:

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Creator: Mauricio Herrera Cuadra

Created: 2006-03-06 03:40:04 UTC

Size: 14.97 KB

patch

obsolete

>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

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Attachments on bug 94123: 63057