head	1.11;
access;
symbols
	RELEASE_4_9_0:1.10
	RELEASE_5_1_0:1.8
	RELEASE_4_8_0:1.8
	RELEASE_5_0_0:1.7
	RELEASE_4_7_0:1.6
	RELEASE_4_6_2:1.4
	RELEASE_4_6_1:1.4
	RELEASE_4_6_0:1.4
	RELEASE_5_0_DP1:1.4
	RELEASE_4_5_0:1.3;
locks; strict;
comment	@# @;


1.11
date	2003.10.14.22.25.59;	author knu;	state Exp;
branches;
next	1.10;

1.10
date	2003.08.22.22.53.54;	author knu;	state Exp;
branches;
next	1.9;

1.9
date	2003.06.26.03.34.44;	author knu;	state Exp;
branches;
next	1.8;

1.8
date	2003.01.29.10.45.59;	author knu;	state Exp;
branches;
next	1.7;

1.7
date	2002.10.06.20.59.13;	author knu;	state Exp;
branches;
next	1.6;

1.6
date	2002.08.03.07.02.10;	author knu;	state Exp;
branches;
next	1.5;

1.5
date	2002.07.07.18.21.43;	author knu;	state Exp;
branches;
next	1.4;

1.4
date	2002.03.12.23.12.03;	author knu;	state Exp;
branches;
next	1.3;

1.3
date	2001.12.21.21.25.16;	author knu;	state Exp;
branches;
next	1.2;

1.2
date	2001.11.28.13.46.31;	author knu;	state Exp;
branches;
next	1.1;

1.1
date	2001.10.24.06.21.52;	author knu;	state Exp;
branches;
next	;


desc
@@


1.11
log
@Update to 0.5.3.
@
text
@bin/biofetch
bin/bioflat
bin/biogetseq
@@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
@@dirrm etc/bioinformatics
%%RUBY_SITELIBDIR%%/bio.rb
%%RUBY_SITELIBDIR%%/bio/alignment.rb
%%RUBY_SITELIBDIR%%/bio/appl/alignfactory.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/rexml.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/wublast.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb
%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb
%%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb
%%RUBY_SITELIBDIR%%/bio/appl/genscan/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb
%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/targetp/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/tmhmm/report.rb
%%RUBY_SITELIBDIR%%/bio/data/aa.rb
%%RUBY_SITELIBDIR%%/bio/data/codontable.rb
%%RUBY_SITELIBDIR%%/bio/data/keggorg.rb
%%RUBY_SITELIBDIR%%/bio/data/na.rb
%%RUBY_SITELIBDIR%%/bio/db.rb
%%RUBY_SITELIBDIR%%/bio/db/aaindex.rb
%%RUBY_SITELIBDIR%%/bio/db/embl.rb
%%RUBY_SITELIBDIR%%/bio/db/embl/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/fantom.rb
%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb
%%RUBY_SITELIBDIR%%/bio/db/gff.rb
%%RUBY_SITELIBDIR%%/bio/db/go.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/genome.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/ko.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/microarray.rb
%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
%%RUBY_SITELIBDIR%%/bio/db/medline.rb
%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
%%RUBY_SITELIBDIR%%/bio/extend.rb
%%RUBY_SITELIBDIR%%/bio/feature.rb
%%RUBY_SITELIBDIR%%/bio/io/brdb.rb
%%RUBY_SITELIBDIR%%/bio/io/das.rb
%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
%%RUBY_SITELIBDIR%%/bio/io/fetch.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb
%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
%%RUBY_SITELIBDIR%%/bio/io/registry.rb
%%RUBY_SITELIBDIR%%/bio/io/sql.rb
%%RUBY_SITELIBDIR%%/bio/location.rb
%%RUBY_SITELIBDIR%%/bio/pathway.rb
%%RUBY_SITELIBDIR%%/bio/reference.rb
%%RUBY_SITELIBDIR%%/bio/sequence.rb
@@dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile
@@dirrm %%RUBY_SITELIBDIR%%/bio/io
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
@@dirrm %%RUBY_SITELIBDIR%%/bio/db
@@dirrm %%RUBY_SITELIBDIR%%/bio/data
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/tmhmm
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/targetp
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl
@@dirrm %%RUBY_SITELIBDIR%%/bio
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/dbget
%%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%%/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%%/ja/BioRuby.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Design.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/KEGG_API.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/TODO.rd.ja
%%PORTDOCS%%%%RUBY_MODDOCDIR%%/ja/Tutorial.rd.ja
%%PORTDOCS%%@@dirrm %%RUBY_MODDOCDIR%%/ja
%%PORTDOCS%%@@dirrm %%RUBY_MODDOCDIR%%
@


1.10
log
@Update to 0.5.2.
@
text
@d65 2
@


1.9
log
@Update to 0.5.0.
@
text
@d9 2
d12 1
d16 1
d18 2
d27 2
d97 1
d101 1
d130 1
@


1.8
log
@Update to 0.4.0.
@
text
@d3 1
a3 1
bin/dbget
d11 1
d18 1
d21 5
d37 1
d44 2
d53 1
d62 1
d64 1
d70 1
d85 4
d90 1
d96 1
d107 1
d112 1
@


1.7
log
@Use RUBY_MOD*.
@
text
@d2 1
d13 1
d17 2
a24 1
%%RUBY_SITELIBDIR%%/bio/db/ddbj.rb
d26 4
d32 4
a35 1
%%RUBY_SITELIBDIR%%/bio/db/genpept.rb
a46 3
%%RUBY_SITELIBDIR%%/bio/db/refseq.rb
%%RUBY_SITELIBDIR%%/bio/db/sptr.rb
%%RUBY_SITELIBDIR%%/bio/db/swissprot.rb
a47 1
%%RUBY_SITELIBDIR%%/bio/db/trembl.rb
d54 3
a60 1
%%RUBY_SITELIBDIR%%/bio/matrix.rb
d64 9
a73 1
@@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
a74 4
@@dirrm %%RUBY_SITELIBDIR%%/bio/data
@@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
@@dirrm %%RUBY_SITELIBDIR%%/bio/db
@@dirrm %%RUBY_SITELIBDIR%%/bio/io
@


1.6
log
@Update to 0.3.9.
@
text
@d64 26
a89 26
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/biofetch.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fasta2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fsplit.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2fasta.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gbtab2mysql.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2nuc.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2pep.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2rb.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gt2fasta.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/pmsearch.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb
%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb
%%PORTDOCS%%@@dirrm %%RUBY_EXAMPLESDIR%%/bio
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ChangeLog
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/README
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/BioRuby.rd.ja
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/Design.rd.ja
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/TODO.rd.ja
%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/ja/Tutorial.rd.ja
%%PORTDOCS%%@@dirrm %%RUBY_DOCDIR%%/bio/ja
%%PORTDOCS%%@@dirrm %%RUBY_DOCDIR%%/bio
@


1.5
log
@Update to 0.3.8.
@
text
@d25 1
@


1.4
log
@Update to 0.3.5.
@
text
@d3 4
d9 3
d13 2
d41 1
a42 1
%%RUBY_SITELIBDIR%%/bio/id.rb
d55 2
a56 2
%%RUBY_SITELIBDIR%%/bio/util/fold.rb
%%RUBY_SITELIBDIR%%/bio/util/hoge.rb
a61 1
@@dirrm %%RUBY_SITELIBDIR%%/bio/util
d68 1
d75 2
@


1.3
log
@Update to 0.3.3.
@
text
@d1 1
d32 3
d36 1
d39 2
d55 1
d63 1
d70 1
@


1.2
log
@Update to 0.3.2.
@
text
@d4 1
@


1.1
log
@Add ruby-bio (BioRuby), an integrated environment for Bioinformatics
written in Ruby.
@
text
@d3 1
d11 2
d20 2
d26 2
d29 1
d31 1
d39 2
d61 5
@