ports/132333: Update port: biology/ruby-bio to 1.3.0
Motomichi Matsuzaki
mzaki at m.u-tokyo.ac.jp
Thu Mar 5 12:30:07 UTC 2009
>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
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby/templates
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators/bioruby
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/generators
+ at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
+ at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
+ at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators
+ at 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
+ at dirrm %%RUBY_SITELIBDIR%%/bio/io/biosql/config
+ at 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
+ at dirrm %%RUBY_SITELIBDIR%%/bio/db/fasta
@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
+ at dirrm %%RUBY_SITELIBDIR%%/bio/db/biosql
@dirrm %%RUBY_SITELIBDIR%%/bio/db
@dirrm %%RUBY_SITELIBDIR%%/bio/data
+ at 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
+ at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/yn00
+ at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/codeml
+ at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/baseml
+ at 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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