bin/bioruby
bin/br_biofetch.rb
bin/br_bioflat.rb
bin/br_biogetseq.rb
bin/br_pmfetch.rb
@unexec if cmp -s %D/etc/bioinformatics/seqdatabase.ini %D/etc/bioinformatics/seqdatabase.ini.sample; then rm -f %D/etc/bioinformatics/seqdatabase.ini; fi
etc/bioinformatics/seqdatabase.ini.sample
@exec [ ! -f %B/etc/bioinformatics/seqdatabase.ini ] && cp %B/%f %B/etc/bioinformatics/seqdatabase.ini
@dirrm etc/bioinformatics
%%RUBY_SITELIBDIR%%/bio.rb
%%RUBY_SITELIBDIR%%/bio/alignment.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
%%RUBY_SITELIBDIR%%/bio/appl/blast/rexml.rb
%%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/report.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/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/spidey/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/targetp/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/tmhmm/report.rb
%%RUBY_SITELIBDIR%%/bio/data/aa.rb
%%RUBY_SITELIBDIR%%/bio/data/codontable.rb
%%RUBY_SITELIBDIR%%/bio/data/na.rb
%%RUBY_SITELIBDIR%%/bio/db/aaindex.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/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/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/reaction.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/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/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/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
@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
@dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
@dirrm %%RUBY_SITELIBDIR%%/bio/db
@dirrm %%RUBY_SITELIBDIR%%/bio/data
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/tmhmm
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/targetp
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/spidey
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
@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
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2tab.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gbtab2mysql.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genes2nuc.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genes2pep.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genes2tab.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genome2rb.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genome2tab.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/goslim.rb
%%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
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/vs-genes.rb
%%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
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/TODO.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja
%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%/ja
%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%