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(-)biology/ruby-bio/Makefile Sun Mar 5 22:07:24 2006 (-5 / +27 lines)
Lines 6-28 Link Here
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#
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#
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PORTNAME=      bio
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PORTNAME=      bio
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PORTVERSION=   0.6.2
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PORTVERSION=   1.0.0
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CATEGORIES=    biology ruby
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CATEGORIES=    biology ruby
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MASTER_SITES=  http://bioruby.org/archive/
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MASTER_SITES=  http://bioruby.org/archive/
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PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}
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PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}
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DISTNAME=      ${PORTNAME}ruby-${PORTVERSION}
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DISTNAME=      ${PORTNAME}ruby-${PORTVERSION}
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DIST_SUBDIR=   ruby
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DIST_SUBDIR=   ruby
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MAINTAINER=    ports@FreeBSD.org
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MAINTAINER=    mauricio@arareko.net
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COMMENT=       Integrated environment for Bioinformatics written in Ruby
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COMMENT=       Integrated environment for Bioinformatics written in Ruby
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OPTIONS=       XMLPARSER       "xmlparser support for faster Blast processing" off \
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               BDB4            "bdb4 support for faster flat file indexing" off \
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               MYSQL           "MySQL database support for BioSQL" off \
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               PGSQL           "PostgreSQL database support for BioSQL" off
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OPTIONSFILE=   ${PORT_DBDIR}/ruby-${PORTNAME}/options
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USE_RUBY=      yes
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USE_RUBY=      yes
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USE_RUBY_SETUP=        yes
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USE_RUBY_SETUP=        yes
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RUBY_SETUP=    install.rb
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RUBY_SETUP=    install.rb
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.include <bsd.port.pre.mk>
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.if defined(WITH_XMLPARSER)
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RUN_DEPENDS+=   ${RUBY_SITEARCHLIBDIR}/xmlparser.so:${PORTSDIR}/textproc/ruby-xmlparser
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.endif
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.if defined(WITH_BDB4)
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RUN_DEPENDS+=   ${RUBY_SITEARCHLIBDIR}/bdb.so:${PORTSDIR}/databases/ruby-bdb
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.endif
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.if defined(WITH_MYSQL)
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RUN_DEPENDS+=   ${RUBY_SITELIBDIR}/DBD/Mysql/Mysql.rb:${PORTSDIR}/databases/ruby-dbd_mysql
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.endif
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.if defined(WITH_PGSQL)
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RUN_DEPENDS+=  ${RUBY_SITELIBDIR}/DBD/Pg/Pg.rb:${PORTSDIR}/databases/ruby-dbd_pg
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.endif
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post-patch:
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post-patch:
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       ${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
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       ${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
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               ${WRKSRC}/doc/Tutorial.rd.ja \
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               ${WRKSRC}/doc/Tutorial.rd \
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               ${WRKSRC}/lib/bio/io/registry.rb
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               ${WRKSRC}/lib/bio/io/registry.rb
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do-install:
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do-install:
Lines 38-44 Link Here
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       ${CP} -R ${WRKSRC}/sample/ ${RUBY_MODEXAMPLESDIR}/
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       ${CP} -R ${WRKSRC}/sample/ ${RUBY_MODEXAMPLESDIR}/
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       ${MKDIR} ${RUBY_MODDOCDIR}/ja
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       ${MKDIR} ${RUBY_MODDOCDIR}/ja
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       ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README ${RUBY_MODDOCDIR}/
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       ${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README ${RUBY_MODDOCDIR}/
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       ${INSTALL_DATA} ${WRKSRC}/doc/*.ja ${RUBY_MODDOCDIR}/ja/
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       ${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${RUBY_MODDOCDIR}/
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       ${INSTALL_DATA} ${WRKSRC}/doc/*.rd.ja ${RUBY_MODDOCDIR}/ja/
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.endif
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.endif
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.include <bsd.port.mk>
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.include <bsd.port.post.mk>
(-)biology/ruby-bio/distinfo Sun Mar 5 22:07:24 2006 (-3 / +3 lines)
Lines 1-3 Link Here
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MD5 (ruby/bioruby-0.6.2.tar.gz) = 68c7ae5aa8562bfe1021d9a5201a9581
1
MD5 (ruby/bioruby-1.0.0.tar.gz) = 5106b71b9b53bce7c3b93df911d2411d
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SHA256 (ruby/bioruby-0.6.2.tar.gz) = 92400eab772f1b1f2943adaa5f2915e0c2c1abc559d486c83780aa62f4d903b5
2
SHA256 (ruby/bioruby-1.0.0.tar.gz) = 7d4255e0a032ef21acea32eb1b3051843b3363008f7a36d7515430e2823b1be3
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SIZE (ruby/bioruby-0.6.2.tar.gz) = 270444
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SIZE (ruby/bioruby-1.0.0.tar.gz) = 573771
(-)biology/ruby-bio/pkg-plist Sun Mar 5 22:07:24 2006 (-32 / +144 lines)
Lines 1-3 Link Here
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bin/bioruby
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bin/br_biofetch.rb
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bin/br_biofetch.rb
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bin/br_bioflat.rb
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bin/br_bioflat.rb
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bin/br_biogetseq.rb
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bin/br_biogetseq.rb
Lines 8-15 Link Here
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@dirrm etc/bioinformatics
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@dirrm etc/bioinformatics
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%%RUBY_SITELIBDIR%%/bio.rb
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%%RUBY_SITELIBDIR%%/bio.rb
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%%RUBY_SITELIBDIR%%/bio/alignment.rb
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%%RUBY_SITELIBDIR%%/bio/alignment.rb
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%%RUBY_SITELIBDIR%%/bio/appl/alignfactory.rb
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%%RUBY_SITELIBDIR%%/bio/command.rb
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%%RUBY_SITELIBDIR%%/bio/db.rb
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%%RUBY_SITELIBDIR%%/bio/feature.rb
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%%RUBY_SITELIBDIR%%/bio/location.rb
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%%RUBY_SITELIBDIR%%/bio/pathway.rb
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%%RUBY_SITELIBDIR%%/bio/reference.rb
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%%RUBY_SITELIBDIR%%/bio/sequence.rb
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%%RUBY_SITELIBDIR%%/bio/shell.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast.rb
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%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb
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%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb
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%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
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%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb
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%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
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%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb
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%%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/report.rb
Lines 17-36 Link Here
17
%%RUBY_SITELIBDIR%%/bio/appl/blast/wublast.rb
33
%%RUBY_SITELIBDIR%%/bio/appl/blast/wublast.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb
34
%%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb
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%%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb
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%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
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%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
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%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
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%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb
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%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb
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%%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb
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%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
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%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
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%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/spidey/report.rb
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%%RUBY_SITELIBDIR%%/bio/appl/spidey/report.rb
Lines 39-105 Link Here
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%%RUBY_SITELIBDIR%%/bio/data/aa.rb
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%%RUBY_SITELIBDIR%%/bio/data/aa.rb
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%%RUBY_SITELIBDIR%%/bio/data/codontable.rb
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%%RUBY_SITELIBDIR%%/bio/data/codontable.rb
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%%RUBY_SITELIBDIR%%/bio/data/na.rb
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%%RUBY_SITELIBDIR%%/bio/data/na.rb
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%%RUBY_SITELIBDIR%%/bio/db.rb
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%%RUBY_SITELIBDIR%%/bio/db/aaindex.rb
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%%RUBY_SITELIBDIR%%/bio/db/aaindex.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl.rb
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%%RUBY_SITELIBDIR%%/bio/db/fantom.rb
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%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
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%%RUBY_SITELIBDIR%%/bio/db/gff.rb
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%%RUBY_SITELIBDIR%%/bio/db/go.rb
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%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
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%%RUBY_SITELIBDIR%%/bio/db/medline.rb
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%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
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%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
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%%RUBY_SITELIBDIR%%/bio/db/rebase.rb
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%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/common.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/common.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/sptr.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/sptr.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/trembl.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/trembl.rb
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%%RUBY_SITELIBDIR%%/bio/db/fantom.rb
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%%RUBY_SITELIBDIR%%/bio/db/embl/uniprot.rb
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%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/common.rb
69
%%RUBY_SITELIBDIR%%/bio/db/genbank/common.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb
71
%%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb
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%%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb
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%%RUBY_SITELIBDIR%%/bio/db/gff.rb
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%%RUBY_SITELIBDIR%%/bio/db/go.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/expression.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/genome.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/genome.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/glycan.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/glycan.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/kgml.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/ko.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/ko.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/microarray.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
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%%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
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%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
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%%RUBY_SITELIBDIR%%/bio/db/medline.rb
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%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
74
%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/atom.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/atom.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/chain.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/chain.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/chemicalcomponent.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/model.rb
89
%%RUBY_SITELIBDIR%%/bio/db/pdb/model.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/pdb.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/pdb.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/residue.rb
91
%%RUBY_SITELIBDIR%%/bio/db/pdb/residue.rb
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%%RUBY_SITELIBDIR%%/bio/db/pdb/utils.rb
92
%%RUBY_SITELIBDIR%%/bio/db/pdb/utils.rb
81
%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
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%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
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%%RUBY_SITELIBDIR%%/bio/extend.rb
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%%RUBY_SITELIBDIR%%/bio/feature.rb
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%%RUBY_SITELIBDIR%%/bio/io/brdb.rb
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%%RUBY_SITELIBDIR%%/bio/io/das.rb
93
%%RUBY_SITELIBDIR%%/bio/io/das.rb
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%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
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%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
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%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
95
%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
96
%%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb
89
%%RUBY_SITELIBDIR%%/bio/io/fetch.rb
97
%%RUBY_SITELIBDIR%%/bio/io/fetch.rb
90
%%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
98
%%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
91
%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
99
%%RUBY_SITELIBDIR%%/bio/io/higet.rb
92
%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
93
%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
94
%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb
100
%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb
95
%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
101
%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
96
%%RUBY_SITELIBDIR%%/bio/io/registry.rb
102
%%RUBY_SITELIBDIR%%/bio/io/registry.rb
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%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb
103
%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb
98
%%RUBY_SITELIBDIR%%/bio/io/sql.rb
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%%RUBY_SITELIBDIR%%/bio/io/sql.rb
99
%%RUBY_SITELIBDIR%%/bio/location.rb
105
%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
100
%%RUBY_SITELIBDIR%%/bio/pathway.rb
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%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
101
%%RUBY_SITELIBDIR%%/bio/reference.rb
107
%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
102
%%RUBY_SITELIBDIR%%/bio/sequence.rb
108
%%RUBY_SITELIBDIR%%/bio/sequence/aa.rb
109
%%RUBY_SITELIBDIR%%/bio/sequence/common.rb
110
%%RUBY_SITELIBDIR%%/bio/sequence/compat.rb
111
%%RUBY_SITELIBDIR%%/bio/sequence/format.rb
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%%RUBY_SITELIBDIR%%/bio/sequence/generic.rb
113
%%RUBY_SITELIBDIR%%/bio/sequence/na.rb
114
%%RUBY_SITELIBDIR%%/bio/shell/core.rb
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%%RUBY_SITELIBDIR%%/bio/shell/demo.rb
116
%%RUBY_SITELIBDIR%%/bio/shell/interface.rb
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%%RUBY_SITELIBDIR%%/bio/shell/object.rb
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%%RUBY_SITELIBDIR%%/bio/shell/web.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/codon.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/emboss.rb
121
%%RUBY_SITELIBDIR%%/bio/shell/plugin/entry.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/flatfile.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/keggapi.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/midi.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/obda.rb
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%%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb
127
%%RUBY_SITELIBDIR%%/bio/shell/rails/Rakefile
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers/application.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers/shell_controller.rb
130
%%RUBY_SITELIBDIR%%/bio/shell/rails/app/helpers/application_helper.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/models/shell_connection.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/layouts/shell.rhtml
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/history.rhtml
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/index.rhtml
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%%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell/show.rhtml
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%%RUBY_SITELIBDIR%%/bio/shell/rails/config/boot.rb
137
%%RUBY_SITELIBDIR%%/bio/shell/rails/config/database.yml
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%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environment.rb
139
%%RUBY_SITELIBDIR%%/bio/shell/rails/config/routes.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/development.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/production.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments/test.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/doc/README_FOR_APP
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/404.html
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/500.html
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.cgi
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.fcgi
148
%%RUBY_SITELIBDIR%%/bio/shell/rails/public/dispatch.rb
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/favicon.ico
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/index.html
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/robots.txt
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/images/icon.png
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/images/rails.png
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/controls.js
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/dragdrop.js
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/effects.js
157
%%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts/prototype.js
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%%RUBY_SITELIBDIR%%/bio/shell/rails/public/stylesheets/main.css
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/about
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/breakpointer
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/console
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/destroy
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/generate
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/plugin
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%%RUBY_SITELIBDIR%%/bio/shell/rails/script/runner
166
%%RUBY_SITELIBDIR%%/bio/shell/rails/script/server
167
%%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance/benchmarker
168
%%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance/profiler
169
%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/reaper
170
%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/spawner
171
%%RUBY_SITELIBDIR%%/bio/shell/rails/script/process/spinner
172
%%RUBY_SITELIBDIR%%/bio/shell/rails/test/test_helper.rb
173
%%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb
174
%%RUBY_SITELIBDIR%%/bio/util/contingency_table.rb
175
%%RUBY_SITELIBDIR%%/bio/util/sirna.rb
176
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/buried.rb
177
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/helix.rb
178
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/hydropathy.rb
179
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/nucleotide.rb
180
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/strand.rb
181
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/taylor.rb
182
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/turn.rb
183
%%RUBY_SITELIBDIR%%/bio/util/color_scheme/zappo.rb
184
@dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme
185
@dirrm %%RUBY_SITELIBDIR%%/bio/util
186
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/test
187
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script/process
188
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script/performance
189
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/script
190
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/stylesheets
191
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/javascripts
192
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public/images
193
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/public
194
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/doc
195
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/config/environments
196
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/config
197
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/shell
198
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views/layouts
199
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/views
200
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/models
201
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/helpers
202
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app/controllers
203
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/app
204
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails
205
@dirrm %%RUBY_SITELIBDIR%%/bio/shell/plugin
206
@dirrm %%RUBY_SITELIBDIR%%/bio/shell
207
@dirrm %%RUBY_SITELIBDIR%%/bio/sequence
103
@dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile
208
@dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile
104
@dirrm %%RUBY_SITELIBDIR%%/bio/io
209
@dirrm %%RUBY_SITELIBDIR%%/bio/io
105
@dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb
210
@dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb
Lines 121-129 Link Here
121
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
226
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
122
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat
227
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat
123
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
228
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
229
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq
124
@dirrm %%RUBY_SITELIBDIR%%/bio/appl
230
@dirrm %%RUBY_SITELIBDIR%%/bio/appl
125
@dirrm %%RUBY_SITELIBDIR%%/bio
231
@dirrm %%RUBY_SITELIBDIR%%/bio
232
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/any2fasta.rb
126
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
233
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
234
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/color_scheme_na.rb
127
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget
235
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget
128
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb
236
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb
129
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb
237
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb
Lines 139-144 Link Here
139
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gt2fasta.rb
247
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gt2fasta.rb
140
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmfetch.rb
248
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmfetch.rb
141
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmsearch.rb
249
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmsearch.rb
250
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/psortplot_html.rb
142
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/ssearch2tab.rb
251
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/ssearch2tab.rb
143
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tdiary.rb
252
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tdiary.rb
144
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tfastx2tab.rb
253
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tfastx2tab.rb
Lines 146-151 Link Here
146
%%PORTDOCS%%@dirrm %%RUBY_MODEXAMPLESDIR%%
255
%%PORTDOCS%%@dirrm %%RUBY_MODEXAMPLESDIR%%
147
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ChangeLog
256
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ChangeLog
148
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/README
257
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/README
258
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/KEGG_API.rd
259
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Tutorial.rd
260
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/Changes-0.7.rd
149
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/BioRuby.rd.ja
261
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/BioRuby.rd.ja
150
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Design.rd.ja
262
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Design.rd.ja
151
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja
263
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja

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