Imported Upstream version 1.5.0

parent a132329a
language: ruby
rvm:
- 2.1.6
- 2.0.0
- 1.9.3
- 1.8.7
- rbx-18mode
env:
- TESTOPTS=-v
gemfile:
- gemfiles/Gemfile.travis-ruby1.9
- gemfiles/Gemfile.travis-ruby1.8
before_install:
- gem update --system 2.1.11
- gem --version
- mkdir /tmp/bioruby
- ruby gemfiles/modify-Gemfile.rb
- ruby gemfiles/prepare-gemspec.rb
matrix:
include:
- rvm: 1.9.2
gemfile: gemfiles/Gemfile.travis-ruby1.9
- rvm: rbx-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby
- rvm: 1.9.3
gemfile: gemfiles/Gemfile.travis-ruby1.9
env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test
- rvm: 1.9.3
gemfile: gemfiles/Gemfile.travis-ruby1.9
env: BIORUBY_RAKE_DEFAULT_TASK=gem-test
- rvm: jruby-18mode
gemfile: gemfiles/Gemfile.travis-jruby1.8
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test
- rvm: 1.8.7
gemfile: gemfiles/Gemfile.travis-ruby1.8
env: TESTOPTS=-v
- rvm: rbx-2.2.3
gemfile: gemfiles/Gemfile.travis-rbx
env: TESTOPTS=-v
- rvm: jruby-18mode
gemfile: gemfiles/Gemfile.travis-jruby1.8
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test
exclude:
- rvm: 1.8.7
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
- rvm: 2.2.2
gemfile: gemfiles/Gemfile.travis-ruby2.2
- rvm: 2.1.6
gemfile: gemfiles/Gemfile.travis-ruby1.9
- rvm: 1.9.3
gemfile: gemfiles/Gemfile.travis-ruby1.8
- rvm: rbx-18mode
env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
- rvm: 2.1.6
gemfile: gemfiles/Gemfile.travis-ruby1.9
allow_failures:
- rvm: rbx-19mode
env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby
- rvm: jruby-18mode
gemfile: gemfiles/Gemfile.travis-jruby1.8
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
allow_failures:
- rvm: rbx-2.2.3
gemfile: gemfiles/Gemfile.travis-rbx
env: TESTOPTS=-v
- rvm: jruby-18mode
gemfile: gemfiles/Gemfile.travis-jruby1.8
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
- rvm: jruby-19mode
gemfile: gemfiles/Gemfile.travis-jruby1.9
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
# uncomment this line if your project needs to run something other than `rake`:
# script: bundle exec rspec spec
......
Copyright (C) 1993-2013 Yukihiro Matsumoto. All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
BioRuby is copyrighted free software by Toshiaki Katayama <k@bioruby.org>.
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:
You can redistribute it and/or modify it under either the terms of the
2-clause BSDL (see the file BSDL), 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
......
$BK\%W%m%0%i%`$O%U%j!<%=%U%H%&%'%"$G$9!%(BGPL (the GNU General
Public License)$B%P!<%8%g%s(B2$B$^$?$O0J2<$K<($9>r7o$GK\%W%m%0%i%`(B
$B$r:FG[I[$G$-$^$9!%(BGPL$B$K$D$$$F$O(BGPL$B%U%!%$%k$r;2>H$7$F2<$5$$!%(B
本プログラムはフリーソフトウェアです.2-clause BSDL
または以下に示す条件で本プログラムを再配布できます
2-clause BSDLについてはBSDLファイルを参照して下さい.
1. $BJ#@=$O@)8B$J$/<+M3$G$9!%(B
1. 複製は制限なく自由です.
2. $B0J2<$N>r7o$N$$$:$l$+$rK~$?$9;~$KK\%W%m%0%i%`$N%=!<%9$r(B
$B<+M3$KJQ99$G$-$^$9!%(B
2. 以下の条件のいずれかを満たす時に本プログラムのソースを
自由に変更できます.
(a) $B%M%C%H%K%e!<%:$K%]%9%H$7$?$j!$:n<T$KJQ99$rAwIU$9$k(B
$B$J$I$NJ}K!$G!$JQ99$r8x3+$9$k!%(B
(a) ネットニューズにポストしたり,作者に変更を送付する
などの方法で,変更を公開する.
(b) $BJQ99$7$?K\%W%m%0%i%`$r<+J,$N=jB0$9$kAH?%FbIt$@$1$G(B
$B;H$&!%(B
(b) 変更した本プログラムを自分の所属する組織内部だけで
使う.
(c) $BJQ99E@$rL@<($7$?$&$(!$%=%U%H%&%'%"$NL>A0$rJQ99$9$k!%(B
$B$=$N%=%U%H%&%'%"$rG[I[$9$k;~$K$OJQ99A0$NK\%W%m%0%i(B
$B%`$bF1;~$KG[I[$9$k!%$^$?$OJQ99A0$NK\%W%m%0%i%`$N%=!<(B
$B%9$NF~<jK!$rL@<($9$k!%(B
(c) 変更点を明示したうえ,ソフトウェアの名前を変更する.
そのソフトウェアを配布する時には変更前の本プログラ
ムも同時に配布する.または変更前の本プログラムのソー
スの入手法を明示する.
(d) $B$=$NB>$NJQ99>r7o$r:n<T$H9g0U$9$k!%(B
(d) その他の変更条件を作者と合意する.
3. $B0J2<$N>r7o$N$$$:$l$+$rK~$?$9;~$KK\%W%m%0%i%`$r%3%s%Q%$(B
$B%k$7$?%*%V%8%'%/%H%3!<%I$d<B9T7A<0$G$bG[I[$G$-$^$9!%(B
3. 以下の条件のいずれかを満たす時に本プログラムをコンパイ
ルしたオブジェクトコードや実行形式でも配布できます.
(a) $B%P%$%J%j$r<u$1<h$C$??M$,%=!<%9$rF~<j$G$-$k$h$&$K!$(B
$B%=!<%9$NF~<jK!$rL@<($9$k!%(B
(a) バイナリを受け取った人がソースを入手できるように,
ソースの入手法を明示する.
(b) $B5!3#2DFI$J%=!<%9%3!<%I$rE:IU$9$k!%(B
(b) 機械可読なソースコードを添付する.
(c) $BJQ99$r9T$C$?%P%$%J%j$OL>A0$rJQ99$7$?$&$(!$%*%j%8%J(B
$B%k$N%=!<%9%3!<%I$NF~<jK!$rL@<($9$k!%(B
(c) 変更を行ったバイナリは名前を変更したうえ,オリジナ
ルのソースコードの入手法を明示する.
(d) $B$=$NB>$NG[I[>r7o$r:n<T$H9g0U$9$k!%(B
(d) その他の配布条件を作者と合意する.
4. $BB>$N%W%m%0%i%`$X$N0zMQ$O$$$+$J$kL\E*$G$"$l<+M3$G$9!%$?(B
$B$@$7!$K\%W%m%0%i%`$K4^$^$l$kB>$N:n<T$K$h$k%3!<%I$O!$$=(B
$B$l$>$l$N:n<T$N0U8~$K$h$k@)8B$,2C$($i$l$k>l9g$,$"$j$^$9!%(B
4. 他のプログラムへの引用はいかなる目的であれ自由です.た
だし,本プログラムに含まれる他の作者によるコードは,そ
れぞれの作者の意向による制限が加えられる場合があります.
$B$=$l$i%U%!%$%k$N0lMw$H$=$l$>$l$NG[I[>r7o$J$I$KIU$$$F$O(B
LEGAL$B%U%!%$%k$r;2>H$7$F$/$@$5$$!%(B
それらファイルの一覧とそれぞれの配布条件などに付いては
LEGALファイルを参照してください.
5. $BK\%W%m%0%i%`$X$NF~NO$H$J$k%9%/%j%W%H$*$h$S!$K\%W%m%0%i(B
$B%`$+$i$N=PNO$N8"Mx$OK\%W%m%0%i%`$N:n<T$G$O$J$/!$$=$l$>(B
$B$l$NF~=PNO$r@8@.$7$??M$KB0$7$^$9!%$^$?!$K\%W%m%0%i%`$K(B
$BAH$_9~$^$l$k$?$a$N3HD%%i%$%V%i%j$K$D$$$F$bF1MM$G$9!%(B
5. 本プログラムへの入力となるスクリプトおよび,本プログラ
ムからの出力の権利は本プログラムの作者ではなく,それぞ
れの入出力を生成した人に属します.また,本プログラムに
組み込まれるための拡張ライブラリについても同様です.
6. $BK\%W%m%0%i%`$OL5J]>Z$G$9!%:n<T$OK\%W%m%0%i%`$r%5%]!<%H(B
$B$9$k0U;V$O$"$j$^$9$,!$%W%m%0%i%`<+?H$N%P%0$"$k$$$OK\%W(B
$B%m%0%i%`$N<B9T$J$I$+$iH/@8$9$k$$$+$J$kB;32$KBP$7$F$b@U(B
$BG$$r;}$A$^$;$s!%(B
6. 本プログラムは無保証です.作者は本プログラムをサポート
する意志はありますが,プログラム自身のバグあるいは本プ
ログラムの実行などから発生するいかなる損害に対しても責
任を持ちません.
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -30,10 +30,10 @@ Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
(WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
Use Ruby 1.9.1 or later.
==== Ruby 1.8.5 or earlier
==== Ruby 1.8.6 or earlier
(WONT_FIX) Problems observed only with Ruby 1.8.5 or earlier will not be
fixed. Note that Ruby 1.8.5 or earlier is no longer supported, as described
(WONT_FIX) Problems observed only with Ruby 1.8.6 or earlier will not be
fixed. Note that Ruby 1.8.6 or earlier is no longer supported, as described
in README.rdoc.
==== Ruby 1.8.2 or earlier
......@@ -41,12 +41,6 @@ in README.rdoc.
(WONT_FIX) In some cases, temporary files and directories may not be
removed because of the lack of FileUtils.remove_entry_secure.
=== Issues about SOAP/WSDL
SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
In addition, because of the API changes in recent SOAP4R, some
classes/modules using SOAP4R may not work.
=== Problem with REXML DoS vulnerability patch before 09-Nov-2008
(WONT_FIX) If you have applied a patch taken from
......@@ -146,53 +140,25 @@ Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
== 3. Known issues and bugs in BioRuby
=== DDBJ Web API related classes (Bio::DDBJ::*, Bio::BLAST::Remote::DDBJ)
The DDBJ Web API is stopping after their system replacement in March 2012.
(See the announcement though it is written only in Japanese:
http://www.ddbj.nig.ac.jp/replace/rp120601-j.html)
Due to the stop of the DDBJ Web API, Bio::DDBJ::* and Bio::BLAST::Remote::DDBJ
which are using the web API can not be used.
=== Bio::Ensembl
Due to the renewal of Ensembl web site, Bio::Ensembl does not work for
the latest Ensembl. For a workaround, use an archive server. For example,
"jul2008.archive.ensembl.org" seems to be the last server before the renewal.
human = Bio::Ensembl.new("Homo_sapiens", "jul2008.archive.ensembl.org")
Alternatively, consider using Ruby Ensembl API.
* http://github.com/jandot/ruby-ensembl-api
=== Bio::DBGET and sample/dbget
=== Bio::UniProtKB
(WONT_FIX) Because the DBGET service have not been publically available for
a long time, we give up support for Bio::DBGET and sample/dbget. Instead,
using Bio::TogoWS or Bio::KEGG::API is recommended.
=== Bio::NCBI::SOAP
It seems that Bio::NCBI::SOAP (in lib/bio/io/ncbisoap.rb) does not work
correctly, even running on Ruby 1.8.x. Instead, use Bio::NCBI::REST.
Bio::UniProtKB should be updated to follow UniProtKB format changes described
in http://www.uniprot.org/docs/sp_news.htm .
=== Bio::KEGG::Taxonomy and sample/demo_kegg_taxonomy.rb
=== Bio::PDB
Bio::KEGG::Taxonomy fails to parse current KEGG taxonomy data file probably
because of the growth of the data size.
Bio::PDB should be updated to follow PDB format version 3.3.
=== Bio::SPTR
=== Bio::Blast::Report
Bio::SPTR should be updated to follow UniProtKB format changes described
in http://www.uniprot.org/docs/sp_news.htm .
NCBI announces that that they are makeing a new version of BLAST XML data
format. BioRuby should support it.
=== http://bioruby.org/cgi-bin/biofetch.rb and Bio::Fetch.query
=== Bio::Blast::Default::Report
BioRuby's default BioFetch server http://bioruby.org/cgi-bin/biofetch.rb is
down for years. Please use other server, such as EBI Dbfetch
(http://www.ebi.ac.uk/Tools/dbfetch/dbfetch).
Due to the stop of the http://bioruby.org/cgi-bin/biofetch.rb service,
Bio::Fetch.query always raises error.
Bio::Blast::Default::Report currently supports legacy BLAST only.
It may be better to support BLAST+ text output format, although NCBI
do not recommend to do so because the format is unstable.
== 4. Compatibility issues with other libraries/extensions
......@@ -206,12 +172,6 @@ know which version is suitable.
BioRuby Shell on Web uses Ruby on Rails, but the author of the document does
not know which version is suitable.
==== SOAP4R with Ruby 1.9
soap4r-ruby1.9 may raise "ununitialized constant XML::SaxParser" error with
some combinations of XML parser libraries. It seems this is a bug of
soap4r-ruby1.9.
== 5. Historical descriptions
=== CVS
......
......@@ -2,7 +2,7 @@
= README.rdoc - README for BioRuby
Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
Copyright (C) 2008 Jan Aerts <jandot@bioruby.org>
Copyright (C) 2011-2012 Naohisa Goto <ng@bioruby.org>
Copyright (C) 2011-2015 Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
* The above statement is limited to this file. See below about BioRuby's
copyright and license.
......@@ -31,7 +31,7 @@ analysis can be executed within the BioRuby script, and the results
can be fully parsed to extract the portion you need. BioRuby supports
major biological database formats and provides many ways for accessing
them through flatfile indexing, SQL, web services etc. Various web
services including KEGG API can be easily utilized by BioRuby.
services can be easily utilized by BioRuby.
== FOR MORE INFORMATION
......@@ -45,6 +45,7 @@ See RELEASE_NOTES.rdoc for news and important changes in this version.
README.rdoc:: This file. General information and installation procedure.
RELEASE_NOTES.rdoc:: News and important changes in this release.
KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
doc/RELEASE_NOTES-1.4.3.rdoc:: News and incompatible changes from 1.4.2 to 1.4.3.
doc/RELEASE_NOTES-1.4.2.rdoc:: News and incompatible changes from 1.4.1 to 1.4.2.
doc/RELEASE_NOTES-1.4.1.rdoc:: News and incompatible changes from 1.4.0 to 1.4.1.
doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
......@@ -55,11 +56,11 @@ doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
doc/Tutorial.rd:: BioRuby Tutorial.
doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
==== BioRuby development
ChangeLog:: History of changes.
doc/ChangeLog-1.4.3:: changes from 1.4.2 to 1.4.3.
doc/ChangeLog-before-1.4.2:: changes before 1.4.2.
doc/ChangeLog-before-1.3.1:: changes before 1.3.1.
README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
......@@ -68,7 +69,6 @@ README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including
doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
==== Sample codes
......@@ -99,13 +99,13 @@ The stable release is freely available from the BioRuby website.
{RubyGems (packaging system for Ruby)}[http://rubygems.org/] version of
the BioRuby package is also available for easy installation.
* http://rubyforge.org/projects/bioruby/
* https://rubygems.org/gems/bio
=== git
If you need the latest development version, this is provided at
* http://github.com/bioruby/bioruby
* https://github.com/bioruby/bioruby
and can be obtained by the following procedure:
......@@ -114,8 +114,9 @@ and can be obtained by the following procedure:
== REQUIREMENTS
* Ruby 1.8.6 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
* Ruby 1.9.3-p194 or later, or Ruby 1.8.7-p358 or later is recommended.
* Ruby 1.8.7 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
* Ruby 2.1.6 or later, or Ruby 2.2.2 or later is recommended.
* This is the final version running on Ruby 1.8, tested with Ruby1.8.7-p374.
* See KNOWN_ISSUES.rdoc for Ruby version specific problems.
......@@ -123,22 +124,20 @@ and can be obtained by the following procedure:
Some optional libraries can be utilized to extend BioRuby's functionality.
If your needs meets the following conditions, install them by using RubyGems,
or download and install from the "Ruby Application Archive" (RAA) at
http://raa.ruby-lang.org/, RubyForge at http://rubyforge.org/, GitHub at
http://github.com/, or the following web sites.
or download and install from the following web sites.
For faster parsing of the BLAST XML output format:
* {RAA:xmlparser}[http://raa.ruby-lang.org/project/xmlparser/]
* {xmlparser}[https://rubygems.org/gems/xmlparser]
* For Ruby 1.8: {gem install xmlparser}[http://rubygems.org/gems/xmlparser]
* For Ruby 1.9: http://www.yoshidam.net/Ruby.html#xmlparser
* For Ruby 1.9 or later: http://www.yoshidam.net/Ruby.html#xmlparser
* In both cases, {The Expat XML Parser}[http://expat.sourceforge.net/]
and C compiler will be required.
Creating faster flatfile index using Berkley DB:
* {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]
(which took over {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/])
(which took over {bdb}[https://github.com/ruby-bdb/bdb])
(No RubyGems available)
* {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required.
......@@ -159,11 +158,6 @@ For parsing PhyloXML format files:
* {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/] and C compiler will be
required.
(Only for Ruby 1.9.x) For using SOAP web services e.g. KEGG API:
* {gem install soap4r-ruby1.9}[https://rubygems.org/gems/soap4r-ruby1.9]
* For Ruby 1.8.x, SOAP4R is bundled within the Ruby 1.8.x release.
== INSTALL
......@@ -174,7 +168,7 @@ If you are using RubyGems, just type
% gem install bio
Alternatively, manually download bio-X.X.X.gem from
http://rubyforge.org/projects/bioruby/ and install it by using gems command.
http://bioruby.org/archive/ and install it by using gems command.
RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier,
download and install RubyGems from http://rubygems.org/ .
......@@ -303,9 +297,9 @@ BioRuby can be freely distributed under the same terms as Ruby.
See the file COPYING (or COPYING.ja written in Japanese).
As written in the file COPYING, see the file LEGAL for files distributed
under different license. For example, setup.rb which comes from
{RAA:setup}[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki
(http://i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1.
under different license. For example, setup.rb which comes from "setup"
developed by Minero Aoki (http://i.loveruby.net/en/projects/setup/) is
licensed under LGPL 2.1.
== REFERENCE
......
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......@@ -157,7 +157,8 @@ HTMLFILES_TUTORIAL = [ TUTORIAL_RD_HTML, TUTORIAL_RD_JA_HTML ]
# Formatting RD to html.
def rd2html(src, dst)
sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css #{src} > #{dst}"
title = File.basename(src)
sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css --html-title=#{title} #{src} > #{dst}"
end
# Tutorial.rd to Tutorial.rd.html
......@@ -187,7 +188,7 @@ task :rechangelog do
# The tag name in the command line should be changed
# after releasing new version, updating ChangeLog,
# and doing "git mv ChangeLog doc/ChangeLog-X.X.X".
sh "git log --stat --summary 1.4.2..HEAD > ChangeLog"
sh "git log --stat --summary 1.4.3..HEAD > ChangeLog"
end
# define mktmpdir
......
......@@ -6,14 +6,35 @@
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: br_biofetch.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
#
begin
require 'rubygems'
rescue LoadError
end
require 'bio/io/fetch'
def require_bio_old_biofetch_emulator(mandatory = true)
begin
require 'bio-old-biofetch-emulator'
rescue LoadError
if mandatory then
$stderr.puts "Error: please install bio-old-biofetch-emulator gem."
exit 1
end
end
end
def default_url
'http://bioruby.org/cgi-bin/biofetch.rb'
end
def another_url
'http://www.ebi.ac.uk/cgi-bin/dbfetch'
end
def usage
default_url = 'http://bioruby.org/cgi-bin/biofetch.rb'
another_url = 'http://www.ebi.ac.uk/cgi-bin/dbfetch'
puts "#{$0} [-s[erver] #{another_url}] db id [style] [format]"
puts " server : URL of the BioFetch CGI (default is #{default_url})"
puts " db : database name (embl, genbank, etc.)"
......@@ -29,18 +50,21 @@ end
case ARGV[0]
when /^--?s/ # User specified server
require_bio_old_biofetch_emulator(false)
ARGV.shift
serv = Bio::Fetch.new(ARGV.shift)
puts serv.fetch(*ARGV)
when /^--?e/ # EBI server
ARGV.shift
serv = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
serv = Bio::Fetch.new(another_url)
puts serv.fetch(*ARGV)
when /^--?r/ # BioRuby server
require_bio_old_biofetch_emulator
ARGV.shift
serv = Bio::Fetch.new('http://bioruby.org/cgi-bin/biofetch.rb')
serv = Bio::Fetch.new(default_url)
puts serv.fetch(*ARGV)
else # Default server
require_bio_old_biofetch_emulator
puts Bio::Fetch.query(*ARGV)
end
......
......@@ -3,18 +3,20 @@
#
Gem::Specification.new do |s|
s.name = 'bio'
s.version = "1.4.3.0001"
s.version = "1.5.0"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
s.homepage = "http://bioruby.org/"
s.rubyforge_project = "bioruby"
s.license = "Ruby"
s.summary = "Bioinformatics library"
s.description = "BioRuby is a library for bioinformatics (biology + information science)."
s.platform = Gem::Platform::RUBY
s.files = [
".travis.yml",
"BSDL",
"COPYING",
"COPYING.ja",
"ChangeLog",
......@@ -33,33 +35,33 @@ Gem::Specification.new do |s|
"bin/br_pmfetch.rb",
"bioruby.gemspec",
"bioruby.gemspec.erb",
"doc/ChangeLog-1.4.3",
"doc/ChangeLog-before-1.3.1",
"doc/ChangeLog-before-1.4.2",
"doc/Changes-0.7.rd",
"doc/Changes-1.3.rdoc",
"doc/KEGG_API.rd",
"doc/KEGG_API.rd.ja",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/RELEASE_NOTES-1.4.1.rdoc",
"doc/RELEASE_NOTES-1.4.2.rdoc",
"doc/RELEASE_NOTES-1.4.3.rdoc",
"doc/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/bioruby.css",
"etc/bioinformatics/seqdatabase.ini",
"extconf.rb",
"gemfiles/Gemfile.travis-jruby1.8",
"gemfiles/Gemfile.travis-jruby1.9",
"gemfiles/Gemfile.travis-rbx",
"gemfiles/Gemfile.travis-ruby1.8",
"gemfiles/Gemfile.travis-ruby1.9",
"gemfiles/Gemfile.travis-ruby2.2",
"gemfiles/modify-Gemfile.rb",
"gemfiles/prepare-gemspec.rb",
"lib/bio.rb",
"lib/bio/alignment.rb",
"lib/bio/appl/bl2seq/report.rb",
"lib/bio/appl/blast.rb",
"lib/bio/appl/blast/ddbj.rb",
"lib/bio/appl/blast/format0.rb",
"lib/bio/appl/blast/format8.rb",
"lib/bio/appl/blast/genomenet.rb",
......@@ -128,6 +130,7 @@ Gem::Specification.new do |s|
"lib/bio/db/embl/swissprot.rb",
"lib/bio/db/embl/trembl.rb",
"lib/bio/db/embl/uniprot.rb",
"lib/bio/db/embl/uniprotkb.rb",
"lib/bio/db/fantom.rb",
"lib/bio/db/fasta.rb",
"lib/bio/db/fasta/defline.rb",
......@@ -163,7 +166,6 @@ Gem::Specification.new do |s|
"lib/bio/db/kegg/orthology.rb",
"lib/bio/db/kegg/pathway.rb",
"lib/bio/db/kegg/reaction.rb",
"lib/bio/db/kegg/taxonomy.rb",
"lib/bio/db/lasergene.rb",
"lib/bio/db/litdb.rb",
"lib/bio/db/medline.rb",
......@@ -195,11 +197,6 @@ Gem::Specification.new do |s|
"lib/bio/io/biosql/biosql.rb",
"lib/bio/io/biosql/config/database.yml",
"lib/bio/io/das.rb",
"lib/bio/io/dbget.rb",
"lib/bio/io/ddbjrest.rb",
"lib/bio/io/ddbjxml.rb",
"lib/bio/io/ebisoap.rb",
"lib/bio/io/ensembl.rb",
"lib/bio/io/fastacmd.rb",
"lib/bio/io/fetch.rb",
"lib/bio/io/flatfile.rb",
......@@ -209,14 +206,10 @@ Gem::Specification.new do |s|
"lib/bio/io/flatfile/index.rb",
"lib/bio/io/flatfile/indexer.rb",
"lib/bio/io/flatfile/splitter.rb",
"lib/bio/io/higet.rb",
"lib/bio/io/hinv.rb",
"lib/bio/io/keggapi.rb",
"lib/bio/io/ncbirest.rb",
"lib/bio/io/ncbisoap.rb",
"lib/bio/io/pubmed.rb",
"lib/bio/io/registry.rb",
"lib/bio/io/soapwsdl.rb",
"lib/bio/io/sql.rb",
"lib/bio/io/togows.rb",
"lib/bio/location.rb",
......@@ -247,13 +240,11 @@ Gem::Specification.new do |s|
"lib/bio/shell/plugin/emboss.rb",
"lib/bio/shell/plugin/entry.rb",
"lib/bio/shell/plugin/flatfile.rb",
"lib/bio/shell/plugin/keggapi.rb",
"lib/bio/shell/plugin/midi.rb",
"lib/bio/shell/plugin/ncbirest.rb",
"lib/bio/shell/plugin/obda.rb",
"lib/bio/shell/plugin/psort.rb",
"lib/bio/shell/plugin/seq.rb",
"lib/bio/shell/plugin/soap.rb",
"lib/bio/shell/plugin/togows.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
......@@ -315,16 +306,15 @@ Gem::Specification.new do |s|
"lib/bio/util/sirna.rb",
"lib/bio/version.rb",
"sample/any2fasta.rb",
"sample/benchmark_clustalw_report.rb",
"sample/biofetch.rb",
"sample/color_scheme_na.rb",
"sample/dbget",
"sample/demo_aaindex.rb",
"sample/demo_aminoacid.rb",
"sample/demo_bl2seq_report.rb",
"sample/demo_blast_report.rb",
"sample/demo_codontable.rb",
"sample/demo_das.rb",
"sample/demo_ddbjxml.rb",
"sample/demo_fasta_remote.rb",
"sample/demo_fastaformat.rb",
"sample/demo_genbank.rb",
......@@ -338,8 +328,6 @@ Gem::Specification.new do |s|
"sample/demo_kegg_glycan.rb",
"sample/demo_kegg_orthology.rb",
"sample/demo_kegg_reaction.rb",
"sample/demo_kegg_taxonomy.rb",
"sample/demo_keggapi.rb",
"sample/demo_litdb.rb",
"sample/demo_locations.rb",
"sample/demo_ncbi_rest.rb",
......@@ -372,7 +360,6 @@ Gem::Specification.new do |s|
"sample/na2aa.rb",
"sample/pmfetch.rb",
"sample/pmsearch.rb",
"sample/psortplot_html.rb",
"sample/seqdatabase.ini",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
......@@ -414,6 +401,7 @@ Gem::Specification.new do |s|
"test/data/blast/b0002.faa.m7",
"test/data/blast/b0002.faa.m8",
"test/data/blast/blastp-multi.m7",
"test/data/clustalw/example1-seqnos.aln",
"test/data/clustalw/example1.aln",
"test/data/command/echoarg2.bat",
"test/data/command/echoarg2.sh",
......@@ -520,10 +508,7 @@ Gem::Specification.new do |s|
"test/network/bio/appl/blast/test_remote.rb",
"test/network/bio/appl/test_blast.rb",
"test/network/bio/appl/test_pts1.rb",
"test/network/bio/io/test_ddbjrest.rb",
"test/network/bio/io/test_ensembl.rb",
"test/network/bio/io/test_pubmed.rb",
"test/network/bio/io/test_soapwsdl.rb",
"test/network/bio/io/test_togows.rb",
"test/network/bio/test_command.rb",
"test/runner.rb",
......@@ -560,9 +545,9 @@ Gem::Specification.new do |s|
"test/unit/bio/db/embl/test_embl.rb",
"test/unit/bio/db/embl/test_embl_rel89.rb",
"test/unit/bio/db/embl/test_embl_to_bioseq.rb",
"test/unit/bio/db/embl/test_sptr.rb",
"test/unit/bio/db/embl/test_uniprot.rb",
"test/unit/bio/db/embl/test_uniprot_new_part.rb",
"test/unit/bio/db/embl/test_uniprotkb.rb",
"test/unit/bio/db/embl/test_uniprotkb_new_part.rb",
"test/unit/bio/db/fasta/test_defline.rb",
"test/unit/bio/db/fasta/test_defline_misc.rb",
"test/unit/bio/db/fasta/test_format_qual.rb",
......@@ -603,11 +588,8 @@ Gem::Specification.new do |s|