3 files changed, 174 insertions, 40 deletions

diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
index d1b610579516..49bf25ed0a6a 100644
--- a/biology/ruby-bio/Makefile
+++ b/biology/ruby-bio/Makefile
@@ -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 @@ do-install:
 	${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 --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo
index 29ab23d903c0..46e87dc3a82c 100644
--- a/biology/ruby-bio/distinfo
+++ b/biology/ruby-bio/distinfo
@@ -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 --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index 7a61592cf7a2..c4131e6a3911 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -1,3 +1,4 @@
+bin/bioruby
 bin/br_biofetch.rb
 bin/br_bioflat.rb
 bin/br_biogetseq.rb
@@ -8,8 +9,23 @@ etc/bioinformatics/seqdatabase.ini.sample
 @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 @@ etc/bioinformatics/seqdatabase.ini.sample
 %%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 @@ etc/bioinformatics/seqdatabase.ini.sample
 %%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 @@ etc/bioinformatics/seqdatabase.ini.sample
 @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 @@ etc/bioinformatics/seqdatabase.ini.sample
 %%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 @@ etc/bioinformatics/seqdatabase.ini.sample
 %%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