1 files changed, 140 insertions, 145 deletions

diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index 0dca4fb103b1..bbaec264ae59 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -1,35 +1,71 @@
-bin/bioruby
-bin/br_biofetch
-bin/br_bioflat
-bin/br_biogetseq
-bin/br_pmfetch
-etc/bioinformatics/seqdatabase.ini.sample
-etc/bioinformatics/seqdatabase.ini
+%%RUBY_EXAMPLESDIR%%/bio/any2fasta.rb
+%%RUBY_EXAMPLESDIR%%/bio/biofetch.rb
+%%RUBY_EXAMPLESDIR%%/bio/color_scheme_na.rb
+%%RUBY_EXAMPLESDIR%%/bio/dbget
+%%RUBY_EXAMPLESDIR%%/bio/demo_aaindex.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_aminoacid.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_bl2seq_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_blast_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_codontable.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_das.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_ddbjxml.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_fasta_remote.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_fastaformat.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_genbank.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_genscan_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_gff1.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_go.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_hmmer_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_compound.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_drug.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_genome.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_glycan.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_orthology.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_reaction.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_taxonomy.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_keggapi.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_litdb.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_locations.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_ncbi_rest.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_nucleicacid.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_pathway.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_prosite.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_psort.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_psort_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_pubmed.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_sequence.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_sirna.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_sosui_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_targetp_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/demo_tmhmm_report.rb
+%%RUBY_EXAMPLESDIR%%/bio/enzymes.rb
+%%RUBY_EXAMPLESDIR%%/bio/fasta2tab.rb
+%%RUBY_EXAMPLESDIR%%/bio/fastagrep.rb
+%%RUBY_EXAMPLESDIR%%/bio/fastasort.rb
+%%RUBY_EXAMPLESDIR%%/bio/fsplit.rb
+%%RUBY_EXAMPLESDIR%%/bio/gb2fasta.rb
+%%RUBY_EXAMPLESDIR%%/bio/gb2tab.rb
+%%RUBY_EXAMPLESDIR%%/bio/gbtab2mysql.rb
+%%RUBY_EXAMPLESDIR%%/bio/genes2nuc.rb
+%%RUBY_EXAMPLESDIR%%/bio/genes2pep.rb
+%%RUBY_EXAMPLESDIR%%/bio/genes2tab.rb
+%%RUBY_EXAMPLESDIR%%/bio/genome2rb.rb
+%%RUBY_EXAMPLESDIR%%/bio/genome2tab.rb
+%%RUBY_EXAMPLESDIR%%/bio/goslim.rb
+%%RUBY_EXAMPLESDIR%%/bio/gt2fasta.rb
+%%RUBY_EXAMPLESDIR%%/bio/na2aa.rb
+%%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb
+%%RUBY_EXAMPLESDIR%%/bio/pmsearch.rb
+%%RUBY_EXAMPLESDIR%%/bio/psortplot_html.rb
+%%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb
+%%RUBY_EXAMPLESDIR%%/bio/tdiary.rb
+%%RUBY_EXAMPLESDIR%%/bio/test_phyloxml_big.rb
+%%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb
+%%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb
+%%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/map.rb
-%%RUBY_SITELIBDIR%%/bio/pathway.rb
-%%RUBY_SITELIBDIR%%/bio/reference.rb
-%%RUBY_SITELIBDIR%%/bio/sequence.rb
-%%RUBY_SITELIBDIR%%/bio/shell.rb
-%%RUBY_SITELIBDIR%%/bio/tree.rb
-%%RUBY_SITELIBDIR%%/bio/version.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/muscle.rb
-%%RUBY_SITELIBDIR%%/bio/appl/probcons.rb
-%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
-%%RUBY_SITELIBDIR%%/bio/appl/pts1.rb
-%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb
-%%RUBY_SITELIBDIR%%/bio/appl/tcoffee.rb
 %%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/blast.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast/ddbj.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
@@ -42,56 +78,53 @@ etc/bioinformatics/seqdatabase.ini
 %%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/gcg/msf.rb
 %%RUBY_SITELIBDIR%%/bio/appl/gcg/seq.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/iprscan/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
 %%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/meme/mast.rb
-%%RUBY_SITELIBDIR%%/bio/appl/meme/motif.rb
 %%RUBY_SITELIBDIR%%/bio/appl/meme/mast/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/meme/motif.rb
+%%RUBY_SITELIBDIR%%/bio/appl/muscle.rb
 %%RUBY_SITELIBDIR%%/bio/appl/paml/baseml.rb
+%%RUBY_SITELIBDIR%%/bio/appl/paml/baseml/report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/paml/codeml.rb
+%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml/rates.rb
+%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml/report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/paml/common.rb
 %%RUBY_SITELIBDIR%%/bio/appl/paml/common_report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/paml/yn00.rb
-%%RUBY_SITELIBDIR%%/bio/appl/paml/baseml/report.rb
-%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml/rates.rb
-%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml/report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/paml/yn00/report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/phylip/alignment.rb
 %%RUBY_SITELIBDIR%%/bio/appl/phylip/distance_matrix.rb
+%%RUBY_SITELIBDIR%%/bio/appl/probcons.rb
+%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
 %%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/pts1.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
 %%RUBY_SITELIBDIR%%/bio/appl/targetp/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/tcoffee.rb
 %%RUBY_SITELIBDIR%%/bio/appl/tmhmm/report.rb
+%%RUBY_SITELIBDIR%%/bio/command.rb
 %%RUBY_SITELIBDIR%%/bio/compat/features.rb
 %%RUBY_SITELIBDIR%%/bio/compat/references.rb
 %%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/fantom.rb
-%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
-%%RUBY_SITELIBDIR%%/bio/db/fastq.rb
-%%RUBY_SITELIBDIR%%/bio/db/gff.rb
-%%RUBY_SITELIBDIR%%/bio/db/go.rb
-%%RUBY_SITELIBDIR%%/bio/db/lasergene.rb
-%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
-%%RUBY_SITELIBDIR%%/bio/db/medline.rb
-%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
-%%RUBY_SITELIBDIR%%/bio/db/newick.rb
-%%RUBY_SITELIBDIR%%/bio/db/nexus.rb
-%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
-%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
-%%RUBY_SITELIBDIR%%/bio/db/rebase.rb
-%%RUBY_SITELIBDIR%%/bio/db/soft.rb
-%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
 %%RUBY_SITELIBDIR%%/bio/db/biosql/biosql_to_biosequence.rb
 %%RUBY_SITELIBDIR%%/bio/db/biosql/sequence.rb
 %%RUBY_SITELIBDIR%%/bio/db/embl/common.rb
@@ -102,11 +135,15 @@ etc/bioinformatics/seqdatabase.ini
 %%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/fantom.rb
+%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta/defline.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta/fasta_to_biosequence.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta/format_fasta.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta/format_qual.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta/qual.rb
+%%RUBY_SITELIBDIR%%/bio/db/fasta/qual_to_biosequence.rb
+%%RUBY_SITELIBDIR%%/bio/db/fastq.rb
 %%RUBY_SITELIBDIR%%/bio/db/fastq/fastq_to_biosequence.rb
 %%RUBY_SITELIBDIR%%/bio/db/fastq/format_fastq.rb
 %%RUBY_SITELIBDIR%%/bio/db/genbank/common.rb
@@ -116,6 +153,8 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/db/genbank/genbank_to_biosequence.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/common.rb
 %%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
@@ -127,9 +166,18 @@ etc/bioinformatics/seqdatabase.ini
 %%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/module.rb
 %%RUBY_SITELIBDIR%%/bio/db/kegg/orthology.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/pathway.rb
 %%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
 %%RUBY_SITELIBDIR%%/bio/db/kegg/taxonomy.rb
+%%RUBY_SITELIBDIR%%/bio/db/lasergene.rb
+%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
+%%RUBY_SITELIBDIR%%/bio/db/medline.rb
+%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
+%%RUBY_SITELIBDIR%%/bio/db/newick.rb
+%%RUBY_SITELIBDIR%%/bio/db/nexus.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
@@ -141,10 +189,18 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/db/phyloxml/phyloxml_elements.rb
 %%RUBY_SITELIBDIR%%/bio/db/phyloxml/phyloxml_parser.rb
 %%RUBY_SITELIBDIR%%/bio/db/phyloxml/phyloxml_writer.rb
+%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
+%%RUBY_SITELIBDIR%%/bio/db/rebase.rb
 %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram/abif.rb
 %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram/chromatogram.rb
 %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
 %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram/scf.rb
+%%RUBY_SITELIBDIR%%/bio/db/soft.rb
+%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
+%%RUBY_SITELIBDIR%%/bio/feature.rb
+%%RUBY_SITELIBDIR%%/bio/io/biosql/ar-biosql.rb
+%%RUBY_SITELIBDIR%%/bio/io/biosql/biosql.rb
+%%RUBY_SITELIBDIR%%/bio/io/biosql/config/database.yml
 %%RUBY_SITELIBDIR%%/bio/io/das.rb
 %%RUBY_SITELIBDIR%%/bio/io/dbget.rb
 %%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
@@ -153,6 +209,12 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb
 %%RUBY_SITELIBDIR%%/bio/io/fetch.rb
 %%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/autodetection.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/buffer.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/splitter.rb
 %%RUBY_SITELIBDIR%%/bio/io/higet.rb
 %%RUBY_SITELIBDIR%%/bio/io/hinv.rb
 %%RUBY_SITELIBDIR%%/bio/io/keggapi.rb
@@ -163,15 +225,11 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb
 %%RUBY_SITELIBDIR%%/bio/io/sql.rb
 %%RUBY_SITELIBDIR%%/bio/io/togows.rb
-%%RUBY_SITELIBDIR%%/bio/io/biosql/ar-biosql.rb
-%%RUBY_SITELIBDIR%%/bio/io/biosql/biosql.rb
-%%RUBY_SITELIBDIR%%/bio/io/biosql/config/database.yml
-%%RUBY_SITELIBDIR%%/bio/io/flatfile/autodetection.rb
-%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
-%%RUBY_SITELIBDIR%%/bio/io/flatfile/buffer.rb
-%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
-%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
-%%RUBY_SITELIBDIR%%/bio/io/flatfile/splitter.rb
+%%RUBY_SITELIBDIR%%/bio/location.rb
+%%RUBY_SITELIBDIR%%/bio/map.rb
+%%RUBY_SITELIBDIR%%/bio/pathway.rb
+%%RUBY_SITELIBDIR%%/bio/reference.rb
+%%RUBY_SITELIBDIR%%/bio/sequence.rb
 %%RUBY_SITELIBDIR%%/bio/sequence/aa.rb
 %%RUBY_SITELIBDIR%%/bio/sequence/adapter.rb
 %%RUBY_SITELIBDIR%%/bio/sequence/common.rb
@@ -182,14 +240,13 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/sequence/generic.rb
 %%RUBY_SITELIBDIR%%/bio/sequence/na.rb
 %%RUBY_SITELIBDIR%%/bio/sequence/quality_score.rb
+%%RUBY_SITELIBDIR%%/bio/sequence/sequence_masker.rb
+%%RUBY_SITELIBDIR%%/bio/shell.rb
 %%RUBY_SITELIBDIR%%/bio/shell/core.rb
 %%RUBY_SITELIBDIR%%/bio/shell/demo.rb
 %%RUBY_SITELIBDIR%%/bio/shell/interface.rb
 %%RUBY_SITELIBDIR%%/bio/shell/irb.rb
 %%RUBY_SITELIBDIR%%/bio/shell/object.rb
-%%RUBY_SITELIBDIR%%/bio/shell/script.rb
-%%RUBY_SITELIBDIR%%/bio/shell/setup.rb
-%%RUBY_SITELIBDIR%%/bio/shell/web.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/blast.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/codon.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/das.rb
@@ -221,10 +278,11 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
 %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
 %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
+%%RUBY_SITELIBDIR%%/bio/shell/script.rb
+%%RUBY_SITELIBDIR%%/bio/shell/setup.rb
+%%RUBY_SITELIBDIR%%/bio/shell/web.rb
+%%RUBY_SITELIBDIR%%/bio/tree.rb
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb
-%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb
-%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme.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
@@ -233,100 +291,39 @@ etc/bioinformatics/seqdatabase.ini
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme/taylor.rb
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme/turn.rb
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme/zappo.rb
+%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis_basic.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/cut_symbol.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded.rb
-%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/enzymes.yaml
-%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand.rb
-%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand_complement.rb
-%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/string_formatting.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/enzymes.yaml
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/cut_range.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/cut_ranges.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range.rb
-%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/vertical_cut_range.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/vertical_cut_range.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
-%%RUBY_SITELIBDIR%%/bio.rb
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ChangeLog
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/README.rdoc
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-0.7.rd
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/KEGG_API.rd
-%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Tutorial.rd
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/vs-genes.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_aaindex.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/dbget
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_aminoacid.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_bl2seq_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_blast_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_codontable.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_das.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_ddbjxml.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_fasta_remote.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_fastaformat.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_genbank.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_genscan_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_gff1.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_go.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_hmmer_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/enzymes.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_compound.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_drug.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_genome.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_glycan.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_orthology.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_reaction.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_kegg_taxonomy.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_keggapi.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_litdb.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_locations.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_ncbi_rest.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_nucleicacid.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_pathway.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_prosite.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_psort.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_psort_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_pubmed.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_sequence.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_sirna.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_sosui_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_targetp_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/demo_tmhmm_report.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/fastagrep.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/fastasort.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/gb2tab.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/gbtab2mysql.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/genes2nuc.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/genes2pep.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/genes2tab.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/genome2rb.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/genome2tab.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/goslim.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/gt2fasta.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/na2aa.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/pmfetch.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/pmsearch.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/psortplot_html.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/ssearch2tab.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/tdiary.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/test_phyloxml_big.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/tfastx2tab.rb
-%%PORTEXAMPLES%%%%RUBY_MODEXAMPLESDIR%%/any2fasta.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand_complement.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/string_formatting.rb
+%%RUBY_SITELIBDIR%%/bio/util/sirna.rb
+%%RUBY_SITELIBDIR%%/bio/version.rb
+bin/bioruby
+bin/br_biofetch
+bin/br_bioflat
+bin/br_biogetseq
+bin/br_pmfetch
+etc/bioinformatics/seqdatabase.ini
+etc/bioinformatics/seqdatabase.ini.sample
 @dirrm etc/bioinformatics
 @dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand
 @dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range
@@ -386,6 +383,4 @@ etc/bioinformatics/seqdatabase.ini
 @dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq
 @dirrm %%RUBY_SITELIBDIR%%/bio/appl
 @dirrm %%RUBY_SITELIBDIR%%/bio
-%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%/ja
-%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%
-%%PORTEXAMPLES%%@dirrm %%RUBY_MODEXAMPLESDIR%%
+@dirrm %%RUBY_EXAMPLESDIR%%/bio