head	1.17;
access;
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	RELEASE_4_10_0:1.11
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	RELEASE_4_9_0:1.10
	RELEASE_5_1_0:1.8
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	RELEASE_4_7_0:1.6
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	RELEASE_5_0_DP1:1.4
	RELEASE_4_5_0:1.3;
locks; strict;
comment	@# @;


1.17
date	2010.12.30.23.08.47;	author pgollucci;	state Exp;
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date	2010.12.27.15.11.50;	author pgollucci;	state Exp;
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1.15
date	2010.06.08.00.18.54;	author pgollucci;	state Exp;
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1.14
date	2007.10.24.01.38.51;	author clsung;	state Exp;
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1.13
date	2006.04.25.22.09.29;	author pav;	state Exp;
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1.12
date	2004.12.25.17.52.46;	author knu;	state Exp;
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date	2003.10.14.22.25.59;	author knu;	state Exp;
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date	2003.08.22.22.53.54;	author knu;	state Exp;
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date	2001.10.24.06.21.52;	author knu;	state Exp;
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next	;


desc
@@


1.17
log
@- Fix pkg-plist, got the wrong version before

Reported by:    pointyhat via pav
@
text
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%%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/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
%%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/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/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/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
@@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/bioruby/generators/bioruby/templates
@@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
@@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators
@@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby
@@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins
@@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor
@@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/biosql/config
@@dirrm %%RUBY_SITELIBDIR%%/bio/io/biosql
@@dirrm %%RUBY_SITELIBDIR%%/bio/io
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/phyloxml
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/fastq
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/fasta
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/biosql
@@dirrm %%RUBY_SITELIBDIR%%/bio/db
@@dirrm %%RUBY_SITELIBDIR%%/bio/data
@@dirrm %%RUBY_SITELIBDIR%%/bio/compat
@@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/phylip
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/yn00
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/codeml
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/baseml
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/meme/mast
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/meme
@@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
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl
@@dirrm %%RUBY_SITELIBDIR%%/bio
@@dirrm %%RUBY_EXAMPLESDIR%%/bio
@@dirrm %%RUBY_DOCDIR%%/bio/ja
@@dirrm %%RUBY_DOCDIR%%/bio
@


1.16
log
@- Update to 1.4.1
- Remove MD5

PR:             ports/153394
Submitted by:   myself (pgollucci)
Approved by:    mauricio@@arareko.net (maintainer)
Sponsored by:   RideCharge Inc. / TaxiMagic
@
text
@d1 7
d394 2
@


1.15
log
@- Update to 1.4.0
- Sort pkg-plist
- seperate NOPORTDOCS and NOPORTEXAMPLES
@
text
@d1 65
a65 7
bin/bioruby
bin/br_biofetch
bin/br_bioflat
bin/br_biogetseq
bin/br_pmfetch
etc/bioinformatics/seqdatabase.ini.sample
etc/bioinformatics/seqdatabase.ini
d67 1
a67 11
%%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
a68 12
%%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
d81 1
d83 2
d89 1
d92 1
d95 1
d97 1
a97 1
%%RUBY_SITELIBDIR%%/bio/appl/meme/mast/report.rb
d99 1
d101 2
a105 3
%%RUBY_SITELIBDIR%%/bio/appl/paml/baseml/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml/rates.rb
%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml/report.rb
d109 2
d112 2
d118 1
d120 1
d126 1
a127 16
%%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
d138 2
d145 2
d156 2
d169 1
d171 1
d174 7
d192 2
d198 6
d212 6
d228 5
a232 9
%%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
d243 2
a249 3
%%RUBY_SITELIBDIR%%/bio/shell/script.rb
%%RUBY_SITELIBDIR%%/bio/shell/setup.rb
%%RUBY_SITELIBDIR%%/bio/shell/web.rb
d281 4
a285 3
%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme.rb
%%RUBY_SITELIBDIR%%/bio/util/sirna.rb
d294 2
a299 4
%%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
d305 1
a309 1
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/vertical_cut_range.rb
d313 2
d316 11
a326 72
%%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
d386 1
a386 3
%%PORTDOCS%%@@dirrm %%RUBY_MODDOCDIR%%/ja
%%PORTDOCS%%@@dirrm %%RUBY_MODDOCDIR%%
%%PORTEXAMPLES%%@@dirrm %%RUBY_MODEXAMPLESDIR%%
@


1.14
log
@- Update to 1.1.0

PR:		ports/117369
Submitted by:	Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp>
Approved by:	maintainer (Mauricio Herrera Cuadra)
@
text
@d2 4
a5 5
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
d7 1
a7 3
@@exec [ ! -f %B/etc/bioinformatics/seqdatabase.ini ] && cp %B/%f %B/etc/bioinformatics/seqdatabase.ini
@@dirrm etc/bioinformatics
%%RUBY_SITELIBDIR%%/bio.rb
d19 1
d33 1
d36 3
d41 1
d53 12
d73 2
d81 1
d95 2
d99 2
d105 7
d114 1
d116 1
d120 1
d140 8
d157 1
d159 1
d165 5
d171 1
d174 1
d176 1
d179 1
d181 1
d184 1
d201 1
d206 18
a223 17
%%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
d226 1
a235 1
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme.rb
d239 5
a248 2
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded.rb
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/enzymes.yaml
d252 2
a256 2
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range.rb
%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/vertical_cut_range.rb
d258 73
a330 3
%%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
d338 4
a341 3
@@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
d349 2
d352 2
d357 2
d360 1
d363 1
d371 6
a388 32
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/any2fasta.rb
%%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_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/KEGG_API.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja
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@


1.13
log
@- Update to 1.0.0
- Provide OPTIONS
- Take maintainership

PR:		ports/94123
Submitted by:	Mauricio Herrera Cuadra <mauricio@@arareko.net>
@
text
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%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
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%%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
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@@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
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%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/BioRuby.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Design.rd.ja
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%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/TODO.rd.ja
@


1.12
log
@Update to 0.6.2.
@
text
@d1 1
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%%RUBY_SITELIBDIR%%/bio/appl/alignfactory.rb
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%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb
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%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
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%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb
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%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
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%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb
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%%RUBY_SITELIBDIR%%/bio/db.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl.rb
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%%RUBY_SITELIBDIR%%/bio/db/fantom.rb
%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank.rb
a73 2
%%RUBY_SITELIBDIR%%/bio/db/gff.rb
%%RUBY_SITELIBDIR%%/bio/db/go.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/microarray.rb
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%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
%%RUBY_SITELIBDIR%%/bio/db/medline.rb
%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
d88 1
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%%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
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%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
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%%RUBY_SITELIBDIR%%/bio/location.rb
%%RUBY_SITELIBDIR%%/bio/pathway.rb
%%RUBY_SITELIBDIR%%/bio/reference.rb
%%RUBY_SITELIBDIR%%/bio/sequence.rb
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@


1.11
log
@Update to 0.5.3.
@
text
@d1 4
a4 3
bin/biofetch
bin/bioflat
bin/biogetseq
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%%RUBY_SITELIBDIR%%/bio/data/keggorg.rb
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@


1.10
log
@Update to 0.5.2.
@
text
@d65 2
@


1.9
log
@Update to 0.5.0.
@
text
@d9 2
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@


1.8
log
@Update to 0.4.0.
@
text
@d3 1
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bin/dbget
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@


1.7
log
@Use RUBY_MOD*.
@
text
@d2 1
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%%RUBY_SITELIBDIR%%/bio/db/ddbj.rb
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%%RUBY_SITELIBDIR%%/bio/db/genpept.rb
a46 3
%%RUBY_SITELIBDIR%%/bio/db/refseq.rb
%%RUBY_SITELIBDIR%%/bio/db/sptr.rb
%%RUBY_SITELIBDIR%%/bio/db/swissprot.rb
a47 1
%%RUBY_SITELIBDIR%%/bio/db/trembl.rb
d54 3
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%%RUBY_SITELIBDIR%%/bio/matrix.rb
d64 9
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@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
a74 4
@@dirrm %%RUBY_SITELIBDIR%%/bio/data
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
@@dirrm %%RUBY_SITELIBDIR%%/bio/db
@@dirrm %%RUBY_SITELIBDIR%%/bio/io
@


1.6
log
@Update to 0.3.9.
@
text
@d64 26
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%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/biofetch.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fasta2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fsplit.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2fasta.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gbtab2mysql.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2nuc.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2pep.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2rb.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gt2fasta.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/pmsearch.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb
%%PORTDOCS%%@@dirrm %%RUBY_EXAMPLESDIR%%/bio
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ChangeLog
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/README
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/BioRuby.rd.ja
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/Design.rd.ja
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/TODO.rd.ja
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/Tutorial.rd.ja
%%PORTDOCS%%@@dirrm %%RUBY_DOCDIR%%/bio/ja
%%PORTDOCS%%@@dirrm %%RUBY_DOCDIR%%/bio
@


1.5
log
@Update to 0.3.8.
@
text
@d25 1
@


1.4
log
@Update to 0.3.5.
@
text
@d3 4
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%%RUBY_SITELIBDIR%%/bio/id.rb
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%%RUBY_SITELIBDIR%%/bio/util/fold.rb
%%RUBY_SITELIBDIR%%/bio/util/hoge.rb
a61 1
@@dirrm %%RUBY_SITELIBDIR%%/bio/util
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@


1.3
log
@Update to 0.3.3.
@
text
@d1 1
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@


1.2
log
@Update to 0.3.2.
@
text
@d4 1
@


1.1
log
@Add ruby-bio (BioRuby), an integrated environment for Bioinformatics
written in Ruby.
@
text
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@

