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- Update to 1.4.1

Browse Source 
- Remove MD5

PR:             ports/153394
Submitted by:   myself (pgollucci)
Approved by:    mauricio@arareko.net (maintainer)
Sponsored by:   RideCharge Inc. / TaxiMagic
This commit is contained in:
Philip M. Gollucci 2010-12-27 15:11:50 +00:00
parent 050837e052
commit c58c954676
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=267000
3 changed files with 143 additions and 149 deletions
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2
biology/ruby-bio/Makefile
View File

@ -6,7 +6,7 @@
#
PORTNAME= bio
PORTVERSION= 1.4.0
PORTVERSION= 1.4.1
CATEGORIES= biology ruby
MASTER_SITES= http://bioruby.org/archive/
PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}

5
biology/ruby-bio/distinfo
View File

@ -1,3 +1,2 @@
MD5 (ruby/bioruby-1.4.0.tar.gz) = bd6437e8a8eae181cc38e95c6cde928b
SHA256 (ruby/bioruby-1.4.0.tar.gz) = fa05edfb7351f1bba4fb29585a9f05ed529f9d8e5360a98fd1ad7676d3cd5324
SIZE (ruby/bioruby-1.4.0.tar.gz) = 1266243
SHA256 (ruby/bioruby-1.4.1.tar.gz) = 4610997ef0350b4d17ccd67a76a1712c2d986168523256eb6de395bfc8a3f15d
SIZE (ruby/bioruby-1.4.1.tar.gz) = 1340224

285
biology/ruby-bio/pkg-plist
View File

@ -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