Attachment #82015 for bug #117369

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Lines 6-12 Link Here

(-)ruby-bio/Makefile (-1 / +1 lines)
6	#	6	#
7		7
8	PORTNAME= bio	8	PORTNAME= bio
9	PORTVERSION= 1.0.0	9	PORTVERSION= 1.1.0
10	CATEGORIES= biology ruby	10	CATEGORIES= biology ruby
11	MASTER_SITES= http://bioruby.org/archive/	11	MASTER_SITES= http://bioruby.org/archive/
12	PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}	12	PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}

Lines 1-3 Link Here

(-)ruby-bio/distinfo (-3 / +3 lines)
1	MD5 (ruby/bioruby-1.0.0.tar.gz) = 5106b71b9b53bce7c3b93df911d2411d	1	MD5 (ruby/bioruby-1.1.0.tar.gz) = d4742051875d3a67623de5f87de65a12
2	SHA256 (ruby/bioruby-1.0.0.tar.gz) = 7d4255e0a032ef21acea32eb1b3051843b3363008f7a36d7515430e2823b1be3	2	SHA256 (ruby/bioruby-1.1.0.tar.gz) = d07a903ac633e381b356dd6429d81d318e3da86bc63b12479b57ec7ead1b22f9
3	SIZE (ruby/bioruby-1.0.0.tar.gz) = 573771	3	SIZE (ruby/bioruby-1.1.0.tar.gz) = 807130




%%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/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/format0.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.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/gcg/msf.rb
%%RUBY_SITELIBDIR%%/bio/appl/gcg/seq.rb
%%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/iprscan/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/phylip/alignment.rb
%%RUBY_SITELIBDIR%%/bio/appl/phylip/distance_matrix.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/db/fasta.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/embl/common.rb
%%RUBY_SITELIBDIR%%/bio/db/embl/embl.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/drug.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/glycan.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/kgml.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/orthology.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/taxonomy.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/io/das.rb
%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
%%RUBY_SITELIBDIR%%/bio/io/ebisoap.rb
%%RUBY_SITELIBDIR%%/bio/io/ensembl.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/ncbisoap.rb
%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
%%RUBY_SITELIBDIR%%/bio/io/registry.rb
%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.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
%%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/psort.rb
%%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb
%%RUBY_SITELIBDIR%%/bio/shell/plugin/soap.rb
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-gem.png
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml
%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml
%%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/taylor.rb
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/turn.rb
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/zappo.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/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/double_stranded.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/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/sequence_range.rb
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/vertical_cut_range.rb
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
%%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
@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand
@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range
@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range
@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded
@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme
@dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme
@dirrm %%RUBY_SITELIBDIR%%/bio/util
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor
@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/appl/sosui
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/phylip
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/iprscan
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/gcg
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat

%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/enzymes.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb

%%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%%

Return to bug 117369

Lines 13-30 Link Here

(-)ruby-bio/pkg-plist (-70 / +82 lines)
13	%%RUBY_SITELIBDIR%%/bio/db.rb	13	%%RUBY_SITELIBDIR%%/bio/db.rb
14	%%RUBY_SITELIBDIR%%/bio/feature.rb	14	%%RUBY_SITELIBDIR%%/bio/feature.rb
15	%%RUBY_SITELIBDIR%%/bio/location.rb	15	%%RUBY_SITELIBDIR%%/bio/location.rb
		16	%%RUBY_SITELIBDIR%%/bio/map.rb
16	%%RUBY_SITELIBDIR%%/bio/pathway.rb	17	%%RUBY_SITELIBDIR%%/bio/pathway.rb
17	%%RUBY_SITELIBDIR%%/bio/reference.rb	18	%%RUBY_SITELIBDIR%%/bio/reference.rb
18	%%RUBY_SITELIBDIR%%/bio/sequence.rb	19	%%RUBY_SITELIBDIR%%/bio/sequence.rb
19	%%RUBY_SITELIBDIR%%/bio/shell.rb	20	%%RUBY_SITELIBDIR%%/bio/shell.rb
		21	%%RUBY_SITELIBDIR%%/bio/tree.rb
20	%%RUBY_SITELIBDIR%%/bio/appl/blast.rb	22	%%RUBY_SITELIBDIR%%/bio/appl/blast.rb
21	%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb	23	%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb
22	%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb	24	%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb
23	%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb	25	%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
24	%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb	26	%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb
25	%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb	27	%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
		28	%%RUBY_SITELIBDIR%%/bio/appl/muscle.rb
		29	%%RUBY_SITELIBDIR%%/bio/appl/probcons.rb
26	%%RUBY_SITELIBDIR%%/bio/appl/psort.rb	30	%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
		31	%%RUBY_SITELIBDIR%%/bio/appl/pts1.rb
27	%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb	32	%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb
		33	%%RUBY_SITELIBDIR%%/bio/appl/tcoffee.rb
28	%%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb	34	%%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb
29	%%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb	35	%%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb
30	%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb	36	%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
Lines 35-44 Link Here
35	%%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb	41	%%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb
36	%%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb	42	%%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb
37	%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb	43	%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
38	%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb	44	%%RUBY_SITELIBDIR%%/bio/appl/gcg/msf.rb
		45	%%RUBY_SITELIBDIR%%/bio/appl/gcg/seq.rb
39	%%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb	46	%%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb
40	%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb	47	%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb
		48	%%RUBY_SITELIBDIR%%/bio/appl/iprscan/report.rb
41	%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb	49	%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
		50	%%RUBY_SITELIBDIR%%/bio/appl/phylip/alignment.rb
		51	%%RUBY_SITELIBDIR%%/bio/appl/phylip/distance_matrix.rb
42	%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb	52	%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
43	%%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb	53	%%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb
44	%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb	54	%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb
Lines 53-64 Link Here
53	%%RUBY_SITELIBDIR%%/bio/db/fasta.rb	63	%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
54	%%RUBY_SITELIBDIR%%/bio/db/gff.rb	64	%%RUBY_SITELIBDIR%%/bio/db/gff.rb
55	%%RUBY_SITELIBDIR%%/bio/db/go.rb	65	%%RUBY_SITELIBDIR%%/bio/db/go.rb
		66	%%RUBY_SITELIBDIR%%/bio/db/lasergene.rb
56	%%RUBY_SITELIBDIR%%/bio/db/litdb.rb	67	%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
57	%%RUBY_SITELIBDIR%%/bio/db/medline.rb	68	%%RUBY_SITELIBDIR%%/bio/db/medline.rb
58	%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb	69	%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
		70	%%RUBY_SITELIBDIR%%/bio/db/newick.rb
		71	%%RUBY_SITELIBDIR%%/bio/db/nexus.rb
59	%%RUBY_SITELIBDIR%%/bio/db/pdb.rb	72	%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
60	%%RUBY_SITELIBDIR%%/bio/db/prosite.rb	73	%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
61	%%RUBY_SITELIBDIR%%/bio/db/rebase.rb	74	%%RUBY_SITELIBDIR%%/bio/db/rebase.rb
		75	%%RUBY_SITELIBDIR%%/bio/db/soft.rb
62	%%RUBY_SITELIBDIR%%/bio/db/transfac.rb	76	%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
63	%%RUBY_SITELIBDIR%%/bio/db/embl/common.rb	77	%%RUBY_SITELIBDIR%%/bio/db/embl/common.rb
64	%%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb	78	%%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb
Lines 72-79 Link Here
72	%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb	86	%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb
73	%%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb	87	%%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb
74	%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb	88	%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb
75	%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
76	%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb	89	%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
		90	%%RUBY_SITELIBDIR%%/bio/db/kegg/drug.rb
77	%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb	91	%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb
78	%%RUBY_SITELIBDIR%%/bio/db/kegg/expression.rb	92	%%RUBY_SITELIBDIR%%/bio/db/kegg/expression.rb
79	%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb	93	%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb
Lines 81-88 Link Here
81	%%RUBY_SITELIBDIR%%/bio/db/kegg/glycan.rb	95	%%RUBY_SITELIBDIR%%/bio/db/kegg/glycan.rb
82	%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb	96	%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb
83	%%RUBY_SITELIBDIR%%/bio/db/kegg/kgml.rb	97	%%RUBY_SITELIBDIR%%/bio/db/kegg/kgml.rb
84	%%RUBY_SITELIBDIR%%/bio/db/kegg/ko.rb	98	%%RUBY_SITELIBDIR%%/bio/db/kegg/orthology.rb
85	%%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb	99	%%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
		100	%%RUBY_SITELIBDIR%%/bio/db/kegg/taxonomy.rb
86	%%RUBY_SITELIBDIR%%/bio/db/pdb/atom.rb	101	%%RUBY_SITELIBDIR%%/bio/db/pdb/atom.rb
87	%%RUBY_SITELIBDIR%%/bio/db/pdb/chain.rb	102	%%RUBY_SITELIBDIR%%/bio/db/pdb/chain.rb
88	%%RUBY_SITELIBDIR%%/bio/db/pdb/chemicalcomponent.rb	103	%%RUBY_SITELIBDIR%%/bio/db/pdb/chemicalcomponent.rb
Lines 93-103 Link Here
93	%%RUBY_SITELIBDIR%%/bio/io/das.rb	108	%%RUBY_SITELIBDIR%%/bio/io/das.rb
94	%%RUBY_SITELIBDIR%%/bio/io/dbget.rb	109	%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
95	%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb	110	%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
		111	%%RUBY_SITELIBDIR%%/bio/io/ebisoap.rb
		112	%%RUBY_SITELIBDIR%%/bio/io/ensembl.rb
96	%%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb	113	%%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb
97	%%RUBY_SITELIBDIR%%/bio/io/fetch.rb	114	%%RUBY_SITELIBDIR%%/bio/io/fetch.rb
98	%%RUBY_SITELIBDIR%%/bio/io/flatfile.rb	115	%%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
99	%%RUBY_SITELIBDIR%%/bio/io/higet.rb	116	%%RUBY_SITELIBDIR%%/bio/io/higet.rb
100	%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb	117	%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb
		118	%%RUBY_SITELIBDIR%%/bio/io/ncbisoap.rb
101	%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb	119	%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
102	%%RUBY_SITELIBDIR%%/bio/io/registry.rb	120	%%RUBY_SITELIBDIR%%/bio/io/registry.rb
103	%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb	121	%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb
Lines 114-175 Link Here
114	%%RUBY_SITELIBDIR%%/bio/shell/core.rb	132	%%RUBY_SITELIBDIR%%/bio/shell/core.rb
115	%%RUBY_SITELIBDIR%%/bio/shell/demo.rb	133	%%RUBY_SITELIBDIR%%/bio/shell/demo.rb
116	%%RUBY_SITELIBDIR%%/bio/shell/interface.rb	134	%%RUBY_SITELIBDIR%%/bio/shell/interface.rb
		135	%%RUBY_SITELIBDIR%%/bio/shell/irb.rb
117	%%RUBY_SITELIBDIR%%/bio/shell/object.rb	136	%%RUBY_SITELIBDIR%%/bio/shell/object.rb
		137	%%RUBY_SITELIBDIR%%/bio/shell/script.rb
		138	%%RUBY_SITELIBDIR%%/bio/shell/setup.rb
118	%%RUBY_SITELIBDIR%%/bio/shell/web.rb	139	%%RUBY_SITELIBDIR%%/bio/shell/web.rb
		140	%%RUBY_SITELIBDIR%%/bio/shell/plugin/blast.rb
119	%%RUBY_SITELIBDIR%%/bio/shell/plugin/codon.rb	141	%%RUBY_SITELIBDIR%%/bio/shell/plugin/codon.rb
		142	%%RUBY_SITELIBDIR%%/bio/shell/plugin/das.rb
120	%%RUBY_SITELIBDIR%%/bio/shell/plugin/emboss.rb	143	%%RUBY_SITELIBDIR%%/bio/shell/plugin/emboss.rb
121	%%RUBY_SITELIBDIR%%/bio/shell/plugin/entry.rb	144	%%RUBY_SITELIBDIR%%/bio/shell/plugin/entry.rb
122	%%RUBY_SITELIBDIR%%/bio/shell/plugin/flatfile.rb	145	%%RUBY_SITELIBDIR%%/bio/shell/plugin/flatfile.rb
123	%%RUBY_SITELIBDIR%%/bio/shell/plugin/keggapi.rb	146	%%RUBY_SITELIBDIR%%/bio/shell/plugin/keggapi.rb
124	%%RUBY_SITELIBDIR%%/bio/shell/plugin/midi.rb	147	%%RUBY_SITELIBDIR%%/bio/shell/plugin/midi.rb
125	%%RUBY_SITELIBDIR%%/bio/shell/plugin/obda.rb	148	%%RUBY_SITELIBDIR%%/bio/shell/plugin/obda.rb
		149	%%RUBY_SITELIBDIR%%/bio/shell/plugin/psort.rb
126	%%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb	150	%%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb
127	%%RUBY_SITELIBDIR%%/bio/shell/rails/Rakefile	151	%%RUBY_SITELIBDIR%%/bio/shell/plugin/soap.rb
128	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers/application.rb	152	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb
129	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers/shell_controller.rb	153	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml
130	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/helpers/application_helper.rb	154	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml
131	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/models/shell_connection.rb	155	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml
132	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/layouts/shell.rhtml	156	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml
133	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/history.rhtml	157	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml
134	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/index.rhtml	158	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif
135	%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/show.rhtml	159	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png
136	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/boot.rb	160	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-gem.png
137	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/database.yml	161	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif
138	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environment.rb	162	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css
139	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/routes.rb	163	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml
140	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/development.rb	164	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb
141	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/production.rb	165	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb
142	%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/test.rb	166	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml
143	%%RUBY_SITELIBDIR%%/bio/shell/rails/doc/README_FOR_APP	167	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml
144	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/404.html	168	%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml
145	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/500.html
146	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.cgi
147	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.fcgi
148	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.rb
149	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/favicon.ico
150	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/index.html
151	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/robots.txt
152	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/images/icon.png
153	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/images/rails.png
154	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/controls.js
155	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/dragdrop.js
156	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/effects.js
157	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/prototype.js
158	%%RUBY_SITELIBDIR%%/bio/shell/rails/public/stylesheets/main.css
159	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/about
160	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/breakpointer
161	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/console
162	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/destroy
163	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/generate
164	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/plugin
165	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/runner
166	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/server
167	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance/benchmarker
168	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance/profiler
169	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/reaper
170	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/spawner
171	%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/spinner
172	%%RUBY_SITELIBDIR%%/bio/shell/rails/test/test_helper.rb
173	%%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb	169	%%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb
174	%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb	170	%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb
175	%%RUBY_SITELIBDIR%%/bio/util/sirna.rb	171	%%RUBY_SITELIBDIR%%/bio/util/sirna.rb
Lines 181-206 Link Here
181	%%RUBY_SITELIBDIR%%/bio/util/color_scheme/taylor.rb	177	%%RUBY_SITELIBDIR%%/bio/util/color_scheme/taylor.rb
182	%%RUBY_SITELIBDIR%%/bio/util/color_scheme/turn.rb	178	%%RUBY_SITELIBDIR%%/bio/util/color_scheme/turn.rb
183	%%RUBY_SITELIBDIR%%/bio/util/color_scheme/zappo.rb	179	%%RUBY_SITELIBDIR%%/bio/util/color_scheme/zappo.rb
		180	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme.rb
		181	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis.rb
		182	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis_basic.rb
		183	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/cut_symbol.rb
		184	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
		185	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
		186	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
		187	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
		188	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
		189	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded.rb
		190	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/enzymes.yaml
		191	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/cut_range.rb
		192	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/cut_ranges.rb
		193	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
		194	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
		195	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
		196	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
		197	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range.rb
		198	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/vertical_cut_range.rb
		199	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
		200	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand.rb
		201	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand_complement.rb
		202	%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/string_formatting.rb
		203	@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand
		204	@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range
		205	@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range
		206	@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded
		207	@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme
184	@dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme	208	@dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme
185	@dirrm %%RUBY_SITELIBDIR%%/bio/util	209	@dirrm %%RUBY_SITELIBDIR%%/bio/util
186	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/test	210	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates
187	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script/process	211	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby
188	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance	212	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators
189	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script	213	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins
190	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/stylesheets	214	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor
191	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts
192	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/images
193	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public
194	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/doc
195	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments
196	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/config
197	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell
198	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/layouts
199	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views
200	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/models
201	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/helpers
202	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers
203	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app
204	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails	215	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails
205	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/plugin	216	@dirrm %%RUBY_SITELIBDIR%%/bio/shell/plugin
206	@dirrm %%RUBY_SITELIBDIR%%/bio/shell	217	@dirrm %%RUBY_SITELIBDIR%%/bio/shell
Lines 219-227 Link Here
219	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui	230	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui
220	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4	231	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4
221	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort	232	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
		233	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/phylip
222	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft	234	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
		235	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/iprscan
223	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer	236	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
224	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan	237	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
		238	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/gcg
225	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta	239	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
226	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw	240	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
227	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat	241	@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat
Lines 233-238 Link Here
233	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb	247	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
234	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb	248	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb
235	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget	249	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget
		250	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/enzymes.rb
236	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb	251	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb
237	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb	252	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb
238	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb	253	%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb
Lines 258-267 Link Here
258	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/KEGG_API.rd	273	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/KEGG_API.rd
259	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Tutorial.rd	274	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Tutorial.rd
260	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-0.7.rd	275	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-0.7.rd
261	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/BioRuby.rd.ja
262	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Design.rd.ja
263	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja	276	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja
264	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/TODO.rd.ja
265	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja	277	%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja
266	%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%/ja	278	%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%/ja
267	%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%	279	%%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%