Date: Thu, 5 Mar 2009 12:21:20 GMT From: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/132333: Update port: biology/ruby-bio to 1.3.0 Message-ID: <200903051221.n25CLKoa064310@www.freebsd.org> Resent-Message-ID: <200903051230.n25CU74Z085276@freefall.freebsd.org>
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>Number: 132333 >Category: ports >Synopsis: Update port: biology/ruby-bio to 1.3.0 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu Mar 05 12:30:06 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: >Organization: >Environment: >Description: I'm sending a patch of FreeBSD ports, biology/ruby-bio, updating to 1.3.0 from 1.1.0. It works fine for me, although I have tested only for very fundamental functions. Please note that the port now depends on ActiveRecord, but I'm not familiar with the framework. Anyway, please update the FreeBSD ports repository. >How-To-Repeat: >Fix: Patch attached with submission follows: diff -ruN ruby-bio.bak/Makefile ruby-bio/Makefile --- ruby-bio.bak/Makefile 2007-10-24 10:38:51.000000000 +0900 +++ ruby-bio/Makefile 2009-03-05 21:01:22.000000000 +0900 @@ -6,7 +6,7 @@ # PORTNAME= bio -PORTVERSION= 1.1.0 +PORTVERSION= 1.3.0 CATEGORIES= biology ruby MASTER_SITES= http://bioruby.org/archive/ PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX} @@ -18,13 +18,12 @@ OPTIONS= XMLPARSER "xmlparser support for faster Blast processing" off \ BDB4 "bdb4 support for faster flat file indexing" off \ - MYSQL "MySQL database support for BioSQL" off \ - PGSQL "PostgreSQL database support for BioSQL" off + ACTIVERECORD "ActiveRecord support for BioSQL" off \ OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNAME}/options USE_RUBY= yes USE_RUBY_SETUP= yes -RUBY_SETUP= install.rb +RUBY_SETUP= setup.rb .include <bsd.port.pre.mk> @@ -34,11 +33,8 @@ .if defined(WITH_BDB4) RUN_DEPENDS+= ${RUBY_SITEARCHLIBDIR}/bdb.so:${PORTSDIR}/databases/ruby-bdb .endif -.if defined(WITH_MYSQL) -RUN_DEPENDS+= ${RUBY_SITELIBDIR}/DBD/Mysql/Mysql.rb:${PORTSDIR}/databases/ruby-dbd_mysql -.endif -.if defined(WITH_PGSQL) -RUN_DEPENDS+= ${RUBY_SITELIBDIR}/DBD/Pg/Pg.rb:${PORTSDIR}/databases/ruby-dbd_pg +.if defined(WITH_ACTIVERECORD) +RUN_DEPENDS+= ${LOCALBASE}/${SPEC_DIR}/activerecord-2.2.2.gemspec:${PORTSDIR}/databases/rubygem-activerecord .endif post-patch: @@ -58,8 +54,8 @@ ${MKDIR} ${RUBY_MODEXAMPLESDIR} ${CP} -R ${WRKSRC}/sample/ ${RUBY_MODEXAMPLESDIR}/ ${MKDIR} ${RUBY_MODDOCDIR}/ja - ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README ${RUBY_MODDOCDIR}/ - ${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${RUBY_MODDOCDIR}/ + ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/*.rdoc ${RUBY_MODDOCDIR}/ + ${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${WRKSRC}/doc/*.rdoc ${RUBY_MODDOCDIR}/ ${INSTALL_DATA} ${WRKSRC}/doc/*.rd.ja ${RUBY_MODDOCDIR}/ja/ .endif diff -ruN ruby-bio.bak/distinfo ruby-bio/distinfo --- ruby-bio.bak/distinfo 2007-10-24 10:38:51.000000000 +0900 +++ ruby-bio/distinfo 2009-03-05 13:05:11.000000000 +0900 @@ -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-1.3.0.tar.gz) = a69f225c9f20851e1b9d2c4a82d026d1 +SHA256 (ruby/bioruby-1.3.0.tar.gz) = 9836d84a9791136c54b483deaaff577895891db58437ef118a9a1a5f802570f8 +SIZE (ruby/bioruby-1.3.0.tar.gz) = 914552 diff -ruN ruby-bio.bak/pkg-plist ruby-bio/pkg-plist --- ruby-bio.bak/pkg-plist 2007-10-24 10:38:51.000000000 +0900 +++ ruby-bio/pkg-plist 2009-03-05 19:59:25.000000000 +0900 @@ -1,8 +1,8 @@ bin/bioruby -bin/br_biofetch.rb -bin/br_bioflat.rb -bin/br_biogetseq.rb -bin/br_pmfetch.rb +bin/br_biofetch +bin/br_bioflat +bin/br_biogetseq +bin/br_pmfetch @unexec if cmp -s %D/etc/bioinformatics/seqdatabase.ini %D/etc/bioinformatics/seqdatabase.ini.sample; then rm -f %D/etc/bioinformatics/seqdatabase.ini; fi etc/bioinformatics/seqdatabase.ini.sample @exec [ ! -f %B/etc/bioinformatics/seqdatabase.ini ] && cp %B/%f %B/etc/bioinformatics/seqdatabase.ini @@ -19,6 +19,7 @@ %%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 +33,15 @@ %%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 +53,15 @@ %%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/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/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 @@ -55,6 +70,8 @@ %%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 @@ -74,15 +91,24 @@ %%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/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 @@ -114,19 +140,57 @@ %%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/biodatabase.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/bioentry.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/bioentry_dbxref.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/bioentry_path.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/bioentry_qualifier_value.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/bioentry_reference.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/bioentry_relationship.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/biosequence.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/comment.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/dbxref.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/dbxref_qualifier_value.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/location.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/location_qualifier_value.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/ontology.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/reference.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/seqfeature.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/seqfeature_dbxref.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/seqfeature_path.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/seqfeature_qualifier_value.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/seqfeature_relationship.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/taxon.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/taxon_name.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/term.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/term_dbxref.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/term_path.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/term_relationship.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/term_relationship_term.rb +%%RUBY_SITELIBDIR%%/bio/io/biosql/term_synonym.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/shell/core.rb @@ -145,27 +209,29 @@ %%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/sirna.rb @@ -207,9 +273,10 @@ @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 +284,18 @@ @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/pdb @dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg @dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank +@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 +303,10 @@ @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/mafft @dirrm %%RUBY_SITELIBDIR%%/bio/appl/iprscan @dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer @@ -247,8 +323,11 @@ %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/demo_sequence.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/enzymes.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fastagrep.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fastasort.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2tab.rb @@ -260,6 +339,7 @@ %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genome2tab.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/goslim.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gt2fasta.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/na2aa.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmfetch.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmsearch.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/psortplot_html.rb @@ -269,10 +349,13 @@ %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/vs-genes.rb %%PORTDOCS%%@dirrm %%RUBY_MODEXAMPLESDIR%% %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ChangeLog -%%PORTDOCS%%%%RUBY_MODDOCDIR%%/README +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/KNOWN_ISSUES.rdoc +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/README.rdoc +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/README_DEV.rdoc %%PORTDOCS%%%%RUBY_MODDOCDIR%%/KEGG_API.rd %%PORTDOCS%%%%RUBY_MODDOCDIR%%/Tutorial.rd %%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-0.7.rd +%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-1.3.rdoc %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja %%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja %%PORTDOCS%%@dirrm %%RUBY_MODDOCDIR%%/ja >Release-Note: >Audit-Trail: >Unformatted:
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