debian/0000755000000000000000000000000012256366277007206 5ustar debian/rules0000755000000000000000000000175012200113662010242 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 # # Uncomment to ignore all test failures (but the tests will run anyway) #export DH_RUBY_IGNORE_TESTS=all # # Uncomment to ignore some test failures (but the tests will run anyway). # Valid values: #export DH_RUBY_IGNORE_TESTS=ruby1.8 ruby1.9.1 require-rubygems # # If you need to specify the .gemspec (eg there is more than one) #export DH_RUBY_GEMSPEC=gem.gemspec %: dh $@ --buildsystem=ruby --with ruby override_dh_auto_build: dh_auto_build docbook-to-man debian/br_biofetch.rb.sgml > br_biofetch.1 docbook-to-man debian/br_bioflat.rb.sgml > br_bioflat.1 docbook-to-man debian/br_biogetseq.rb.sgml > br_biogetseq.1 docbook-to-man debian/br_pmfetch.rb.sgml > br_pmfetch.1 override_dh_auto_clean: dh_auto_clean rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 override_dh_auto_install: dh_auto_install for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$$(echo $$FILE | sed 's/\.rb$$//'); \ mv $$FILE $$BINNAME; \ done debian/br_biofetch.rb.sgml0000644000000000000000000001224611722725161012733 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> David"> Nusinow"> January 31, 2005"> 1"> dnusinow@debian.org"> BIORUBY"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2005 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; biofetch client &dhpackage; server db id DESCRIPTION This manual page documents briefly the &dhpackage;. &dhpackage; is a very simple biofetch client. You can connect to a biofetch server and retrieve database entries including sequence information. OPTIONS Specify the URL of the BioFetch CGI (default is http://bioruby.org/cgi-bin/biofetch.rb) Use the EBI server at http://www.ebi.ac.uk/cgi-bin/dbfetch Use the BioRuby server at http://bioruby.org/cgi-bin/biofetch.rb Database name. This includes options like refseq, genbank, embl, swissprot, etc. This option depends on which biofetch server you are using. entry id \'raw\' or \'html\' (default is \'raw\') Output format ('default, 'fasta', 'etc') SEE ALSO bar (1), baz (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/br_pmfetch.rb.sgml0000644000000000000000000002021311722725161012567 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> David"> Nusinow"> January 31, 2005"> 1"> dnusinow@debian.org"> BIORUBY"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2005 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; PubMed Client &dhpackage; "query string" &dhpackage; DESCRIPTION This manual page documents briefly the &dhpackage;. &dhpackage; is a command line program to query PubMed. It can take a variety of options (documented below) to restrict your search query, which is specified by the query string. OPTIONS Query string for PubMed search. Title of the article to search. Journal title to search. Journal volume to search. Journal issue to search. First page number of the article to search. Author name to search. MeSH term to search. Summary output format. Options are endnote, medline, bibitem, bibtex, report, abstract nature, science, genome_res, genome_biol, nar, current, trends, cell. Output only a list of PudMed IDs. Number of articles to retrieve at the maximum. Starting number of articles to retrieve. Sort method for the summary output. Options are author, journal, pub+date. Search articles published within recent # of days. Search articles published after the date YYYY/MM/DD. Search articles published before the date YYYY/MM/DD. Output help and then exit. Output example usages and then exit. Output version number and then exit. SEE ALSO The following pages have information on the PubMed search options: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/watch0000644000000000000000000000013311722725161010220 0ustar version=3 http://pkg-ruby-extras.alioth.debian.org/cgi-bin/gemwatch/bio .*/bio-(.*).tar.gz debian/source/0000755000000000000000000000000012200264132010456 5ustar debian/source/format0000644000000000000000000000001411722725161011700 0ustar 3.0 (quilt) debian/br_biogetseq.rb.sgml0000644000000000000000000001023411722725161013125 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> David"> Nusinow"> January 31, 2005"> 1"> dnusinow@debian.org"> BIORUBY"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2005 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; ODBA Sequence Retrieval &dhpackage; DESCRIPTION This manual page documents briefly the &dhpackage;. &dhpackage; is an ODBC sequence retrieval program. Simply point it at the database of interest, with an optional namespace, and give it the sequence id that you want, and it will retrieve it. OPTIONS Specify the database to query (required). Specify the namespace to query. Specify the ID of the sequence to be retrieved. AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/ruby-bio.docs0000644000000000000000000000010112200264132011550 0ustar README* KNOWN_ISSUES.rdoc doc etc/bioinformatics/seqdatabase.ini debian/copyright0000644000000000000000000002155012200264132011114 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: bio Source: http://www.bioruby.org/ Files: * Copyright: 2000-2013 Toshiaki Katayama 2002-2013 Naohisa Goto 2000-2008 Mitsuteru C. Nakao 2000-2008 Jan Aerts 2000-2006 Yoshinori K. Okuji 2001-2005 Shuichi Kawashima 2002 Hiroshi Suga , 2003 Masumi Itoh 2003-2005 Natsuhiro Ichinose 2004-2006 Alex Gutteridge 2004-2006 Daniel Amelang 2005 Masashi Fujita , 2005-2006 Shuji SHIGENOBU 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon 2006 Christian M Zmasek 2006-2008 Ryan Raaum 2007 Center for Biomedical Research Informatics, University of Minnesota 2008 Raoul Jean Pierre Bonnal 2008 Adam Kraut 2008 Michael D. Barton 2008-2010 Pjotr Prins 2009 Diana Jaunzeikare 2009 Anthony Underwood 2009-2010 Kozo Nishida 2011 Tomoaki NISHIYAMA License: GPL-2 or Ruby BioRuby is copyrighted free software by Toshiaki Katayama . You can redistribute it and/or modify it under either the terms of the GPL version 2 (see the file GPL), or the conditions below. Files: setup.rb Copyright: 2000-2006 Minero Aoki License: LGPL-2.1 Files: sample/any2fasta.rb Copyright: 2006 Pjotr Prins License: GPL-2+ Files: sample/biofetch.rb: Copyright: 2002-2004 KATAYAMA Toshiaki License: GPL-2+ Files: sample/enzymes.rb: Copyright: 2006 Pjotr Prins 2006 Trevor Wennblom License: GPL-2+ Files: sample/fasta2tab.rb sample/fsplit.rb sample/gb2tab.rb sample/genes2nuc.rb sample/genes2pep.rb sample/genes2tab.rb sample/genome2tab.rb sample/gt2fasta.rb sample/ssearch2tab.rb sample/tfastx2tab.rb sample/vs-genes.rb Copyright: 2001 KATAYAMA Toshiaki License: GPL-2+ Files: sample/fastagrep.rb sample/fastasort.rb sample/na2aa.rb Copyright: 2008 KATAYAMA Toshiaki 2008 Pjotr Prins License: GPL-2+ Files: sample/gb2fasta.rb Copyright: 2001 KATAYAMA Toshiaki 2002 Yoshinori K. Okuji License: GPL-2+ Files: sample/gbtab2mysql.rb sample/genome2rb.rb sample/pmfetch.rb sample/pmsearch.rb Copyright: 2002 KATAYAMA Toshiaki License: GPL-2+ Files: sample/tdiary.rb Copyright: 2003 KATAYAMA Toshiaki 2003 Mitsuteru C. Nakao 2003 Itoshi NIKAIDO 2003 Takeya KASUKAWA License: GPL-2+ Files: test/data/uniprot/p53_human.uniprot Copyright: none These files are marked to be copyrighted by the UniProt Consortium, but this applies to the UniProt database as a whole, not to the individual records. License: not-the-CC-BY-ND-3.0 Despite the following statement: . Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms Distributed under the Creative Commons Attribution-NoDerivs License . The above files, as individual records, are not copyrighted. The statement is for the UniProt as a whole. Files: debian/* Copyright: Copyright 2011 Lucas Nussbaum License: GPL-2 or Ruby License: GPL-2 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. License: LGPL-2.1 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU Lesser General Public License version 2.1 can be found in the file `/usr/share/common-licenses/LGPL-2.1'. License: Ruby BioRuby is copyrighted free software by Toshiaki Katayama . You can redistribute it and/or modify it under either the terms of the GPL version 2 (see the file GPL), or the conditions below: . 1. You may make and give away verbatim copies of the source form of the software without restriction, provided that you duplicate all of the original copyright notices and associated disclaimers. . 2. You may modify your copy of the software in any way, provided that you do at least ONE of the following: . a) place your modifications in the Public Domain or otherwise make them Freely Available, such as by posting said modifications to Usenet or an equivalent medium, or by allowing the author to include your modifications in the software. . b) use the modified software only within your corporation or organization. . c) give non-standard binaries non-standard names, with instructions on where to get the original software distribution. . d) make other distribution arrangements with the author. . 3. You may distribute the software in object code or binary form, provided that you do at least ONE of the following: . a) distribute the binaries and library files of the software, together with instructions (in the manual page or equivalent) on where to get the original distribution. . b) accompany the distribution with the machine-readable source of the software. . c) give non-standard binaries non-standard names, with instructions on where to get the original software distribution. . d) make other distribution arrangements with the author. . 4. You may modify and include the part of the software into any other software (possibly commercial). But some files in the distribution are not written by the author, so that they are not under these terms. . For the list of those files and their copying conditions, see the file LEGAL. . 5. The scripts and library files supplied as input to or produced as output from the software do not automatically fall under the copyright of the software, but belong to whomever generated them, and may be sold commercially, and may be aggregated with this software. . 6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. debian/control0000644000000000000000000000245312256365726010613 0ustar Source: ruby-bio Section: ruby Priority: optional Maintainer: Debian Ruby Extras Maintainers Uploaders: Lucas Nussbaum , Cédric Boutillier Build-Depends: debhelper (>= 7.0.50~), gem2deb (>= 0.5.0~), ruby-libxml (>= 2.7.0-2~), ruby-test-unit Build-Depends-Indep: docbook-to-man, rdtool Standards-Version: 3.9.5 Vcs-Git: git://anonscm.debian.org/pkg-ruby-extras/ruby-bio.git Vcs-Browser: http://anonscm.debian.org/gitweb?p=pkg-ruby-extras/ruby-bio.git;a=summary Homepage: http://www.bioruby.org/ XS-Ruby-Versions: all Package: ruby-bio Architecture: all XB-Ruby-Versions: ${ruby:Versions} Depends: ${shlibs:Depends}, ${misc:Depends}, ruby | ruby-interpreter Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Description: Ruby tools for computational molecular biology BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation. debian/upstream0000644000000000000000000000074711762671776011005 0ustar Reference: Author: Naohisa Goto and Pjotr Prins and Mitsuteru Nakao and Raoul Bonnal and Jan Aerts and Toshiaki Katayama Title: "BioRuby: bioinformatics software for the Ruby programming language" Journal: Bioinformatics Year: 2010 Volume: 26 Number: 20 Pages: 2617-9 DOI: 10.1093/bioinformatics/btq475 PMID: 20739307 URL: http://bioinformatics.oxfordjournals.org/content/26/20/2617 eprint: http://bioinformatics.oxfordjournals.org/content/26/20/2617.full.pdf+html debian/patches/0000755000000000000000000000000012200270322010603 5ustar debian/patches/disable_tests_using_chi2.patch0000644000000000000000000000206712200263724016600 0ustar Description: deactivate tests in test/unit/bio/sequence using chi2 These tests using randomness fail from time to time (1% of failure). They need to be disabled not to create false positive FTBFS. Author: Cédric Boutillier Origin: vendor Bug: https://github.com/bioruby/bioruby/issues/56 Last-Update: 2013-08-06 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- a/test/unit/bio/sequence/test_common.rb +++ b/test/unit/bio/sequence/test_common.rb @@ -319,11 +319,15 @@ end private :randomize_equiprobability + ## Debian patch: test deactivated because randomly failing def test_randomize_equiprobability + omit "test randomly failing skipped" randomize_equiprobability { |seq| seq.randomize } end + ## Debian patch: test deactivated because randomly failing def test_randomize_with_hash_equiprobability + omit "test randomly failing skipped" hash = { 'c' => 4, 'g' => 3, 't' => 2, 'a' => 1 } randomize_equiprobability { |seq| seq.randomize(hash) } end debian/patches/fix_shebang_for_examples.patch0000644000000000000000000000045311772054261016666 0ustar Description: Ensure we have the correct shebang in examples Origin: vendor Last-Update: 2012-06-23 --- a/sample/biofetch.rb +++ b/sample/biofetch.rb @@ -1,4 +1,4 @@ -#!/usr/proj/bioruby/bin/ruby +#!/usr/bin/env ruby # # biofetch.rb : BioFetch server (interface to GenomeNet/DBGET via KEGG API) # debian/patches/series0000644000000000000000000000012412200270322012015 0ustar disable_tests_using_chi2.patch fix_shebang_for_examples.patch remove_rubygems.patch debian/patches/remove_rubygems.patch0000644000000000000000000000054612200270322015043 0ustar Description: remove use of rubygems in bin/bioruby Origin: vendor Forwarded: not-needed Last-Update: 2013-08-06 --- a/bin/bioruby +++ b/bin/bioruby @@ -9,12 +9,7 @@ # $Id:$ # -begin - require 'rubygems' - gem 'bio', '>= 1.1.0' -rescue LoadError - require 'bio' -end +require 'bio' require 'bio/shell' # required to run commands (getseq, ls etc.) debian/compat0000644000000000000000000000000211722725161010370 0ustar 7 debian/ruby-bio.examples0000644000000000000000000000001111722725161012452 0ustar sample/* debian/br_bioflat.rb.sgml0000644000000000000000000001757211722725161012577 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> David"> Nusinow"> January 31, 2005"> 1"> dnusinow@debian.org"> BIORUBY"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2005 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; OBDA flat file indexer Search: &dhpackage; &dhpackage; --location DIR --dbname DBNAME KEYWORDS Create index: &dhpackage; Update index: &dhpackage; Show namespaces: &dhpackage; &dhpackage; &dhpackage; DESCRIPTION This manual page documents briefly the &dhpackage;. &dhpackage; is an OBDA flat file indexer. OPTIONS Search a database for keywords. Only valid with the --search option. Set the search namespace. You can set this option multiple times to specify more than one namespace. Create an index. Specify the directory. Specify the name of the database. Set the primary and secondarynamespace of the index. Default primary/secondary namespaces depend on the format of the flatfiles. Only valid with the --create option. Add secondary namespaces to the default specification. You can use this option many times. Only valid with the --create option. Update an index Sort an index. You can set this to a path to an external sorting program, or BUILTIN to use the builtin sort module. This option is only valid with --create (or --update) and --type flat options. Re-read all flatfiles and update whole index. This option is only valid with the --update option. Display the namespaces for an index file. AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/changelog0000644000000000000000000002001512256366066011052 0ustar ruby-bio (1.4.3.0001-2) unstable; urgency=low * debian/ruby-tests.rb: choose to define external encoding if Encoding is defined instead of checking version of Ruby, which was too strict. (Closes: #720240) * Tighten dependency on ruby-libxml and gem2deb to ensure Ruby 2.0 support. (Closes: #730644) * Bump Standards-Version to 3.9.5 (no changes needed) -- Cédric Boutillier Tue, 24 Dec 2013 21:18:56 +0100 ruby-bio (1.4.3.0001-1) unstable; urgency=low * Imported Upstream version 1.4.3.0001 * debian/control: + remove obsolete DM-Upload-Allowed flag + use canonical URI in Vcs-* fields + build-depend on ruby-test-unit + bump Standards-Version to 3.9.4 (no changes needed) + update my email address + drop transitional packages * debian/patches: + drop disable-test-soap.patch, fixed upstream + drop fix_definition_CutSymbol_in_test_cut_symbol.patch, fixed upstream + drop do_not_rely_on_keys_order_for_hashes.patch, fixed upstream + omit chi2 tests instead of commenting them out + add remove_rubygems.patch: remove requirement on rubygems from bin/bioruby * debian/ruby-tests.rb: do not exclude manually tests requiring network in ruby-tests.rb, now moved to a dedicated directory by upstream * remove debian/source/lintian-overrides, related to transitional packages * install KNOWN_ISSUES.rdoc as documentation * provide more complete copyright information -- Cédric Boutillier Tue, 06 Aug 2013 23:19:36 +0200 ruby-bio (1.4.2-3) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add citation information according to https://wiki.debian.org/UpstreamMetadata (Closes: #675061) [ Cédric Boutillier ] * Add myself to Uploaders: * Bump Standards-Version: to 3.9.3 (no changes needed) * Update debian/copyright to cover also setup.rb, sample/* and test/data/uniprot/p53_human.uniprot * debian/patches: + add disable_tests_using_chi2.patch, disabling randomly failing tests + add do_not_rely_on_keys_order_for_hashes.patch, fixing FTBFS (Closes: #674337) + add fix_shebang_for_examples.patch, ensuring the shebang in sample/biofetch.rb is correct * Build-depend on gem2deb >= 0.3.0 * Register HTML tutorials in doc-base -- Cédric Boutillier Mon, 25 Jun 2012 11:34:26 +0200 ruby-bio (1.4.2-2) unstable; urgency=low * Remove some tests depending on a access to the Internet. Closes: #654985 * Add fix_definition_CutSymbol_in_test_cut_symbol.patch to ensure that Bio::RestrictionEnzyme::CutSymbol is defined * Set to extra the priority of transitional packages * Depends on ruby-libxml instead of libxml-ruby -- Cédric Boutillier Fri, 17 Feb 2012 15:22:29 +0100 ruby-bio (1.4.2-1) unstable; urgency=low * New upstream version. + Fixes build failure. Closes: #642035. * fix typos in debian/copyright. * document disable-test-soap.patch. -- Lucas Nussbaum Sun, 25 Sep 2011 11:01:38 +0200 ruby-bio (1.4.1-2) unstable; urgency=low * Switch to gem2deb packaging. Rename binary and source package, introduce transitional packages. -- Lucas Nussbaum Thu, 28 Jul 2011 17:25:55 +0200 bioruby (1.4.1-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.1 (no changes needed) - Added Recommends: hmmer, mafft, muscle, probcons, sim4, t-coffee which are called in lib/bio/appl - Added Suggests: clustalw (non-free), emboss (large and thus not always wanted on the system just for BioRuby development) * Source format 3.0 (quilt) -- Andreas Tille Thu, 25 Nov 2010 16:04:31 +0100 bioruby (1.4.0-2) unstable; urgency=low * Fixed long description Closes: #453022 * New upstream version from past upload just Closes: #524180 -- Andreas Tille Fri, 22 Jan 2010 16:26:50 +0100 bioruby (1.4.0-1) unstable; urgency=low * New upstream version -- Andreas Tille Thu, 21 Jan 2010 11:42:04 +0100 bioruby (1.3.1-1) unstable; urgency=low * debian/control: - Group maintenance in Debian Med team - Added myself as uploader - Standards-Version: 3.8.3 (no changes needed) - Debhelper >= 7.1 - Homepage and Vcs fileds -- Andreas Tille Sun, 04 Oct 2009 09:15:28 +0200 bioruby (1.1.0-1) unstable; urgency=low * New upstream version + Bioruby is now distributed under the same terms as ruby itself. This gives you the option of using the GPL or a similar copyleft license. See /usr/share/doc/libbio-ruby/copyright for details on the alternate license. + Lots of new and obsolete classes, see the upstream changelog for details + BioRuby shell rewritten to utilize the rails generators + Many bugfixes * Re-work build system to utilize install.rb instead of my custom rules file + Enable unit tests in the build + Don't hardcode the binary names when hacking off the .rb suffix. Use wildcards and a for loop to rename them + Remove the libbio-ruby1.8.dirs file. The directories get installed by the install.rb now + The docs are built by install.rb now, so don't do custom stuff for them in debian/rules + Move building the manpages to the build-stamp target, rather than the build target + Add ruby to build-depends -- David Nusinow Sun, 22 Jul 2007 18:42:39 -0400 bioruby (1.0.0-1) unstable; urgency=low * New upstream version * Add the bioruby shell program * Add the Changes-0.7.html doc describing updates since 0.6.x * Bump standards version to 3.7.2.0. No changes needed. * Bump debhelper compat to 5 * Move debhelper to build-depends from build-depends-indep -- David Nusinow Thu, 17 Aug 2006 00:28:21 +0000 bioruby (0.6.4-1) unstable; urgency=low * New upstream release + siRNA designer class is contributed by Itoshi Nikaido. (lib/bio/util/sirna.rb) + fastacmd wrapper is contributed by Shinji Shigenobu. (lib/bio/io/fastacmd.rb) + bl2seq parser is contributed by Tomoaki Nishiyama. (lib/bio/appl/bl2seq/report.rb) + new application execution factory is provided. (lib/bio/command.rb) + FlatFile class can accept Blast results, Spidey, Blat, Sim4 and some KEGG formats (KO, GLYCAN, REACTION) + some methods are added to SPTr class proposed by Luca Pireddu. (lib/bio/db/embl/sptr.rb) + external2go parser is added. (lib/bio/db/go.rb) + improved amino/nucleic data classes to have some handy methods. (lib/bio/data/) + fixed hmmer parser (by Masashi Fujita) and remote execution of blast and fasta using GenomeNet. + some English documentations are added. (doc/) * Re-organize debian/rules handling of docs + Ship new English tutorial and KEGG_API. These are turned to html with rd2 + Put document building commands in the build target instead of configure + Add commands to remove generated documents in the clean target + Put package building commands in binary-indep where they belong * Add build-dependency on rdtool to build html docs using rd2 * Minor debian/copyright cleanup to get rid of stupid lintian warning about boilerplate * Change Build-Depends to Build-Depends-Indep * Update standards version to 3.6.2. No changes needed. * Add ruby1.8 to recommends for libbio-ruby1.8 -- David Nusinow Thu, 1 Sep 2005 14:04:35 -0400 bioruby (0.6.2-3) unstable; urgency=low * Add watch file -- David Nusinow Thu, 7 Apr 2005 22:12:44 -0400 bioruby (0.6.2-2) unstable; urgency=low * Depend on libruby1.8 instead of ruby1.8 to bring in line with ruby policy * Add Recommends on blast2 for local blast * Depend on docbook-to-man; closes: #302360 -- David Nusinow Tue, 1 Feb 2005 00:25:45 -0500 bioruby (0.6.2-1) unstable; urgency=low * Initial Release. -- David Nusinow Mon, 31 Jan 2005 11:11:55 -0500 debian/ruby-bio.doc-base.ja0000644000000000000000000000057711772563214012727 0ustar Document: ruby-bio-tutorial-ja Author: Toshiaki Katayama, Naohisa Goto Title: Tutorial for BioRuby project (Japanese) Abstract: This is a tutorial in Japanese for the BioRuby project, an open source bioinformatics library for Ruby. Section: Programming/Ruby Format: HTML Index: /usr/share/doc/ruby-bio/doc/Tutorial.rd.ja.html Files: /usr/share/doc/ruby-bio/doc/Tutorial.rd.ja.html debian/ruby-bio.doc-base0000644000000000000000000000060211772563160012323 0ustar Document: ruby-bio-tutorial Author: Toshiaki Katayama, Pjotr Prins, Naohisa Goto and others Title: Tutorial for BioRuby project Abstract: This is a tutorial in English for the BioRuby project, an open source bioinformatics library for Ruby. Section: Programming/Ruby Format: HTML Index: /usr/share/doc/ruby-bio/doc/Tutorial.rd.html Files: /usr/share/doc/ruby-bio/doc/Tutorial.rd.html debian/ruby-tests.rb0000644000000000000000000000017412224225055011635 0ustar Encoding.default_external = "UTF-8" if defined? Encoding Dir['test/{unit,functional}/**/test_*.rb'].each { |f| require f } debian/ruby-bio.manpages0000644000000000000000000000000411722725161012431 0ustar *.1