Date: Thu, 23 Dec 2010 08:03:38 GMT From: "Philip M. Gollucci" <pgollucci@p6m7g8.com> To: FreeBSD-gnats-submit@FreeBSD.org Cc: mauricio@arareko.net Subject: ports/153394: [PATCH] biology/ruby18-bio: update to 1.4.1 Message-ID: <201012230803.oBN83cao050165@frieza.p6m7g8.net> Resent-Message-ID: <201012230810.oBN8A9la075950@freefall.freebsd.org>
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>Number: 153394 >Category: ports >Synopsis: [PATCH] biology/ruby18-bio: update to 1.4.1 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Thu Dec 23 08:10:09 UTC 2010 >Closed-Date: >Last-Modified: >Originator: Philip M. Gollucci >Release: FreeBSD 9.0-CURRENT amd64 >Organization: RideCharge Inc / TaxiMagic >Environment: System: FreeBSD frieza.p6m7g8.net 9.0-CURRENT FreeBSD 9.0-CURRENT #0: Tue Oct 12 00:51:25 UTC 2010 >Description: - Update to 1.4.1 Port maintainer (mauricio@arareko.net) is cc'd. Generated with FreeBSD Port Tools 0.99 >How-To-Repeat: >Fix: --- ruby18-bio-1.4.1.patch begins here --- Index: Makefile =================================================================== RCS file: /home/ncvs/ports/biology/ruby-bio/Makefile,v retrieving revision 1.20 diff -u -u -r1.20 Makefile --- Makefile 8 Jun 2010 00:18:54 -0000 1.20 +++ Makefile 23 Dec 2010 05:21:59 -0000 @@ -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} Index: distinfo =================================================================== RCS file: /home/ncvs/ports/biology/ruby-bio/distinfo,v retrieving revision 1.18 diff -u -u -r1.18 distinfo --- distinfo 8 Jun 2010 00:18:54 -0000 1.18 +++ distinfo 23 Dec 2010 05:22:09 -0000 @@ -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 Index: pkg-plist =================================================================== RCS file: /home/ncvs/ports/biology/ruby-bio/pkg-plist,v retrieving revision 1.15 diff -u -u -r1.15 pkg-plist --- pkg-plist 8 Jun 2010 00:18:54 -0000 1.15 +++ pkg-plist 23 Dec 2010 07:57:24 -0000 @@ -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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ @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 --- ruby18-bio-1.4.1.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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