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Code Issues Releases Activity

- Update to 1.0.0

Browse Source 
- Provide OPTIONS
- Take maintainership

PR:		ports/94123
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
This commit is contained in:
Pav Lucistnik 2006-04-25 22:09:29 +00:00
parent 1db56a4dea
commit dc8e5f28fa
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=160479
3 changed files with 174 additions and 40 deletions
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32
biology/ruby-bio/Makefile
View File

@ -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>

6
biology/ruby-bio/distinfo
View File

@ -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

176
biology/ruby-bio/pkg-plist
View File

@ -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