Date: Tue, 08 Jun 2010 00:26:18 +0000 From: "Philip M. Gollucci" <pgollucci@p6m7g8.com> To: "Philip M. Gollucci" <pgollucci@FreeBSD.org> Cc: cvs-ports@FreeBSD.org, cvs-all@FreeBSD.org, ports-committers@FreeBSD.org Subject: Re: cvs commit: ports/biology/ruby-bio Makefile distinfo pkg-plist Message-ID: <4C0D8E2A.6090605@p6m7g8.com> In-Reply-To: <201006080018.o580Isvc074070@repoman.freebsd.org> References: <201006080018.o580Isvc074070@repoman.freebsd.org>
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Appologies, didn't mean to step on any toes, I was looking at the wrong list of ports. I thought this a ruby@ one. If you would like this backed out, let me. On 06/08/10 00:18, Philip M. Gollucci wrote: > pgollucci 2010-06-08 00:18:54 UTC > > FreeBSD ports repository > > Modified files: > biology/ruby-bio Makefile distinfo pkg-plist > Log: > - Update to 1.4.0 > - Sort pkg-plist > - seperate NOPORTDOCS and NOPORTEXAMPLES > > Revision Changes Path > 1.20 +5 -4 ports/biology/ruby-bio/Makefile > 1.18 +3 -3 ports/biology/ruby-bio/distinfo > 1.15 +180 -68 ports/biology/ruby-bio/pkg-plist > > http://cvsweb.FreeBSD.org/ports/biology/ruby-bio/Makefile.diff?r1=1.19&r2=1.20&f=h > | --- ports/biology/ruby-bio/Makefile 2007/10/24 01:38:51 1.19 > | +++ ports/biology/ruby-bio/Makefile 2010/06/08 00:18:54 1.20 > | @@ -2,11 +2,11 @@ > | # Date created: 24 October 2001 > | # Whom: Akinori MUSHA aka knu <knu@idaemons.org> > | # > | -# $FreeBSD: /usr/local/www/cvsroot/FreeBSD/ports/biology/ruby-bio/Makefile,v 1.19 2007/10/24 01:38:51 clsung Exp $ > | +# $FreeBSD: /usr/local/www/cvsroot/FreeBSD/ports/biology/ruby-bio/Makefile,v 1.20 2010/06/08 00:18:54 pgollucci Exp $ > | # > | > | PORTNAME= bio > | -PORTVERSION= 1.1.0 > | +PORTVERSION= 1.4.0 > | CATEGORIES= biology ruby > | MASTER_SITES= http://bioruby.org/archive/ > | PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX} > | @@ -24,7 +24,6 @@ OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNA > | > | USE_RUBY= yes > | USE_RUBY_SETUP= yes > | -RUBY_SETUP= install.rb > | > | .include <bsd.port.pre.mk> > | > | @@ -54,11 +53,13 @@ do-install: > | ${CP} -p ${PREFIX}/${f}.sample ${PREFIX}/${f}; \ > | fi > | .endfor > | -.if !defined(NOPORTDOCS) > | +.if !defined(NOPORTEXAMPLES) > | ${MKDIR} ${RUBY_MODEXAMPLESDIR} > | ${CP} -R ${WRKSRC}/sample/ ${RUBY_MODEXAMPLESDIR}/ > | +.endif > | +.if !defined(NOPORTDOCS) > | ${MKDIR} ${RUBY_MODDOCDIR}/ja > | - ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README ${RUBY_MODDOCDIR}/ > | + ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README.rdoc ${RUBY_MODDOCDIR}/ > | ${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${RUBY_MODDOCDIR}/ > | ${INSTALL_DATA} ${WRKSRC}/doc/*.rd.ja ${RUBY_MODDOCDIR}/ja/ > | .endif > http://cvsweb.FreeBSD.org/ports/biology/ruby-bio/distinfo.diff?r1=1.17&r2=1.18&f=h > | --- ports/biology/ruby-bio/distinfo 2007/10/24 01:38:51 1.17 > | +++ ports/biology/ruby-bio/distinfo 2010/06/08 00:18:54 1.18 > | @@ -1,3 +1,3 @@ > | -MD5 (ruby/bioruby-1.1.0.tar.gz) = d4742051875d3a67623de5f87de65a12 > | -SHA256 (ruby/bioruby-1.1.0.tar.gz) = d07a903ac633e381b356dd6429d81d318e3da86bc63b12479b57ec7ead1b22f9 > | -SIZE (ruby/bioruby-1.1.0.tar.gz) = 807130 > | +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 > http://cvsweb.FreeBSD.org/ports/biology/ruby-bio/pkg-plist.diff?r1=1.14&r2=1.15&f=h > | --- ports/biology/ruby-bio/pkg-plist 2007/10/24 01:38:51 1.14 > | +++ ports/biology/ruby-bio/pkg-plist 2010/06/08 00:18:54 1.15 > | @@ -1,13 +1,10 @@ > | bin/bioruby > | -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 > | +bin/br_biofetch > | +bin/br_bioflat > | +bin/br_biogetseq > | +bin/br_pmfetch > | etc/bioinformatics/seqdatabase.ini.sample > | -@exec [ ! -f %B/etc/bioinformatics/seqdatabase.ini ] && cp %B/%f %B/etc/bioinformatics/seqdatabase.ini > | -@dirrm etc/bioinformatics > | -%%RUBY_SITELIBDIR%%/bio.rb > | +etc/bioinformatics/seqdatabase.ini > | %%RUBY_SITELIBDIR%%/bio/alignment.rb > | %%RUBY_SITELIBDIR%%/bio/command.rb > | %%RUBY_SITELIBDIR%%/bio/db.rb > | @@ -19,6 +16,7 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%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 > | @@ -32,10 +30,15 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%RUBY_SITELIBDIR%%/bio/appl/sim4.rb > | %%RUBY_SITELIBDIR%%/bio/appl/tcoffee.rb > | %%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/blast/ddbj.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/blast/genomenet.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/blast/ncbioptions.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/blast/remote.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blast/report.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blast/rexml.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/blast/rpsblast.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blast/wublast.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb > | %%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb > | @@ -47,6 +50,18 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%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/meme/mast.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/meme/motif.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/meme/mast/report.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/paml/baseml.rb > | +%%RUBY_SITELIBDIR%%/bio/appl/paml/codeml.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/psort/report.rb > | @@ -55,12 +70,15 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%RUBY_SITELIBDIR%%/bio/appl/spidey/report.rb > | %%RUBY_SITELIBDIR%%/bio/appl/targetp/report.rb > | %%RUBY_SITELIBDIR%%/bio/appl/tmhmm/report.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/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 > | @@ -74,18 +92,32 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%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 > | %%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb > | +%%RUBY_SITELIBDIR%%/bio/db/embl/embl_to_biosequence.rb > | +%%RUBY_SITELIBDIR%%/bio/db/embl/format_embl.rb > | %%RUBY_SITELIBDIR%%/bio/db/embl/sptr.rb > | %%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/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/fastq/fastq_to_biosequence.rb > | +%%RUBY_SITELIBDIR%%/bio/db/fastq/format_fastq.rb > | %%RUBY_SITELIBDIR%%/bio/db/genbank/common.rb > | %%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb > | +%%RUBY_SITELIBDIR%%/bio/db/genbank/format_genbank.rb > | %%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb > | +%%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/kegg/brite.rb > | +%%RUBY_SITELIBDIR%%/bio/db/kegg/common.rb > | %%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb > | %%RUBY_SITELIBDIR%%/bio/db/kegg/drug.rb > | %%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb > | @@ -105,6 +137,14 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%RUBY_SITELIBDIR%%/bio/db/pdb/pdb.rb > | %%RUBY_SITELIBDIR%%/bio/db/pdb/residue.rb > | %%RUBY_SITELIBDIR%%/bio/db/pdb/utils.rb > | +%%RUBY_SITELIBDIR%%/bio/db/phyloxml/phyloxml.xsd > | +%%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/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/io/das.rb > | %%RUBY_SITELIBDIR%%/bio/io/dbget.rb > | %%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb > | @@ -114,21 +154,34 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%RUBY_SITELIBDIR%%/bio/io/fetch.rb > | %%RUBY_SITELIBDIR%%/bio/io/flatfile.rb > | %%RUBY_SITELIBDIR%%/bio/io/higet.rb > | +%%RUBY_SITELIBDIR%%/bio/io/hinv.rb > | %%RUBY_SITELIBDIR%%/bio/io/keggapi.rb > | +%%RUBY_SITELIBDIR%%/bio/io/ncbirest.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/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/sequence/aa.rb > | +%%RUBY_SITELIBDIR%%/bio/sequence/adapter.rb > | %%RUBY_SITELIBDIR%%/bio/sequence/common.rb > | %%RUBY_SITELIBDIR%%/bio/sequence/compat.rb > | +%%RUBY_SITELIBDIR%%/bio/sequence/dblink.rb > | %%RUBY_SITELIBDIR%%/bio/sequence/format.rb > | +%%RUBY_SITELIBDIR%%/bio/sequence/format_raw.rb > | %%RUBY_SITELIBDIR%%/bio/sequence/generic.rb > | %%RUBY_SITELIBDIR%%/bio/sequence/na.rb > | +%%RUBY_SITELIBDIR%%/bio/sequence/quality_score.rb > | %%RUBY_SITELIBDIR%%/bio/shell/core.rb > | %%RUBY_SITELIBDIR%%/bio/shell/demo.rb > | %%RUBY_SITELIBDIR%%/bio/shell/interface.rb > | @@ -145,29 +198,32 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%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/ncbirest.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/plugin/togows.rb > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb > | +%%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml > | +%%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/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 > | @@ -177,29 +233,101 @@ etc/bioinformatics/seqdatabase.ini.sampl > | %%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.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/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.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/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 > | +%%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 > | +@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 > | @@ -207,9 +335,10 @@ etc/bioinformatics/seqdatabase.ini.sampl > | @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/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 > | @@ -217,13 +346,21 @@ etc/bioinformatics/seqdatabase.ini.sampl > | @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 > | @@ -231,6 +368,12 @@ etc/bioinformatics/seqdatabase.ini.sampl > | @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 > | @@ -243,37 +386,6 @@ etc/bioinformatics/seqdatabase.ini.sampl > | @dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq > | @dirrm %%RUBY_SITELIBDIR%%/bio/appl > | @dirrm %%RUBY_SITELIBDIR%%/bio > | -%%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 > | %%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%/ja > | %%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%% > | +%%PORTEXAMPLES%%@dirrm %%RUBY_MODEXAMPLESDIR%% - -- - ------------------------------------------------------------------------ 1024D/DB9B8C1C B90B FBC3 A3A1 C71A 8E70 3F8C 75B8 8FFB DB9B 8C1C Philip M. Gollucci (pgollucci@p6m7g8.com) c: 703.336.9354 VP Apache Infrastructure; Member, Apache Software Foundation Committer, FreeBSD Foundation Consultant, P6M7G8 Inc. Sr. System Admin, Ridecharge Inc. Work like you don't need the money, love like you'll never get hurt, and dance like nobody's watching. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (FreeBSD) iD8DBQFMDY4qdbiP+9ubjBwRAk93AJ9aNQ7wq/1grtT/ikpVpfVyzGF6ewCfRnAb 8LjyoU3pfE+CZyCmmHaLXHE= =8oFZ -----END PGP SIGNATURE-----
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