[BioRuby-cvs] bioruby README,1.9,1.10

Sun Sep 25 20:48:06 EDT 2005

Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv14898

Modified Files:
	README 
Log Message:
* rewrited -- ruby 1.6 is no longer supported, instructions for rubygems
  are included etc.

Index: README
===================================================================
RCS file: /home/repository/bioruby/bioruby/README,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** README	9 Aug 2005 11:43:02 -0000	1.9
--- README	26 Sep 2005 00:48:04 -0000	1.10
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*** 1,29 ****

  = BioRuby

! BioRuby project aims to implement integrated environment for Bioinformatics.

! Object oriented scripting language Ruby has many good points suitable for
! bioinfomatics research.  Powerful regular expressions like Perl, purely
! object oriented, simple and very clean syntax -- easy to learn for beginners,
! easy to use for biologists, powerful enough for developers.

- In BioRuby, you can retrieve biological database entries from flat files,
- internet web servers and local relational databases.  These database entries
- can be parsed to extract any information you need.  Biological sequences are
- treated with Ruby's powerful string methods and regular expressions.  Daily
- tools like Blast, Fasta and Hmmer programs can be executed and the results
- are fully parsed to extract scores and/or alignments.  BioRuby also supports
- some databases and web services developed in Japan such as KEGG, AAindex,
- and DBGET etc.

! == WHERE TO GET

! * WWW -- ((<URL:http://bioruby.org/>))

-     http://bioruby.org/archive/

! * CVS -- ((<URL:http://cvs.bioruby.org/>))

      % cvs -d :pserver:anonymous at cvs.bioruby.org:/export/cvs login
--- 1,56 ----
+ =begin
+ 
+   $Id$
+ 
+   Copyright (C) 2001-2005 Toshiaki Katayama <k at bioruby.org>

  = BioRuby

! BioRuby is an open source Ruby library for developing bioinformatics
! software.  Object oriented scripting language Ruby has many features
! suitable for bioinfomatics research, for example, clear syntax to
! express complex objects, regular expressions for text handling as
! powerful as Perl's, a wide variety of libraries including web service
! etc.  As the syntax of the Ruby language is simple and very clean, we
! believe that it is easy to learn for beginners, easy to use for
! biologists, and also powerful enough for the software developers.

! In BioRuby, you can retrieve biological database entries from flat
! files, internet web servers and local relational databases.  These
! database entries can be parsed to extract information you need.
! Biological sequences can be treated with the fulfilling methods of the
! Ruby's String class and with regular expressions.  Daily tools like
! Blast, Fasta, Hmmer and many other softwares for the biological
! 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 the BioRuby.

+ == FOR MORE INFORMATION

! BioRuby's official website is at ((<URL:http://bioruby.org/>)).
! You will find links to the related resouces including downloads,
! mailing lists, Wiki documentations etc. in the top page.

!   * ((<URL:http://bioruby.org/>))

! == WHERE TO OBTAIN
! 
! --- WWW
! 
! The stable release is freely available from the BioRuby website.
! 
!   * ((<URL:http://bioruby.org/archive/>))
! 
! --- CVS
! 
! If you need the latest development version, anonymous CVS is provided at
! 
!   * ((<URL:http://cvs.bioruby.org/>))
! 
! and can be obtained by the following procedure.

      % cvs -d :pserver:anonymous at cvs.bioruby.org:/export/cvs login
***************
*** 31,65 ****
      % cvs -d :pserver:anonymous at cvs.bioruby.org:/export/cvs co bioruby

  == REQUIREMENTS

! * Ruby 1.6.6 or newer -- ((<URL:http://www.ruby-lang.org/>))

  == OPTIONAL REQUIREMENTS

! * Ruby library -- ((<URL:http://raa.ruby-lang.org/>))

!   * [RAA:strscan] for parsing Blast default output.
!   * [RAA:rexml] for parsing Blast XML output and using DAS.
!   * [RAA:xmlparser] can be used for faster Blast XML parsing.
!   * [RAA:ruby-dbi] and at least one driver from [RAA:mysql-ruby],
!     [RAA:postgres], [RAA:oracle] to use with BioSQL.
!   * [RAA:bdb] for faster flat file indexing.
!   * [RAA:pp] for pretty print in debug.
!   * [RAA:soap4r] (version >= 1.4.8.1) for KEGG API. Note that libraries
!     which SOAP4R depends such as [RAA:date2], [RAA:devel-logger],
!     [RAA:http-access] (version >= j) with one of [RAA:xmlscan], [RAA:rexml],
!     [RAA:rexml-stable], [RAA:xmlparser], [RAA:nqxml] are also needed.

!   Note that 'strscan', 'rexml', 'pp', 'date2' and 'xmlscan' are 
!   included in the Ruby 1.8.0 distibution (you don't need to install
!   them by yourself).

! * External applications can be used if installed

!   * Blast (version >= 2.2.5) for blast execution on local computer
!   * FASTA for fasta, ssearch execution on local computer
!   * HMMER for hmmsearch, hmmpfam execution on local computer

--- 58,92 ----
      % cvs -d :pserver:anonymous at cvs.bioruby.org:/export/cvs co bioruby

+ --- RubyGems
+ 
+ ((<RubyGems|URL:http://rubyforge.org/projects/rubygems/>)) version of
+ the BioRuby package is also available for easy installation.
+ 
+   * ((<URL:http://rubyforge.org/projects/bioruby/>))
+ 

  == REQUIREMENTS

! * Ruby 1.8.2 or later -- ((<URL:http://www.ruby-lang.org/>))

  == OPTIONAL REQUIREMENTS

! Some optional libraries can be utilized to extend BioRuby's functionality.
! If your needs meets the following conditions, install them from the "Ruby
! Application Archive" at ((<URL:http://raa.ruby-lang.org/>)).

! For faster parsing of the BLAST XML output format:

!   * [RAA:xmlparser]

! Creating faster flatfile index using Berkley DB:

!   * [RAA:bdb]
! 
! Accessing BioSQL database created by other Open Bio* libraries:
! 
!   * [RAA:ruby-dbi] and at least one driver from [RAA:mysql-ruby],
!     [RAA:postgres], [RAA:oracle]

***************
*** 74,78 ****
    # ruby install.rb install

! If you are using Mac OS X, you should use 'sudo' command instead of 'su'.

    % ruby install.rb config
--- 101,106 ----
    # ruby install.rb install

! If your operating system supports 'sudo' command (such as Mac OS X),
! try the following procedure instead of the above.

    % ruby install.rb config
***************
*** 80,84 ****
    % sudo ruby install.rb install

! You can try

    % ruby install.rb --help
--- 108,116 ----
    % sudo ruby install.rb install

! You can run tests by
! 
!   % ruby install.rb test
! 
! and run

    % ruby install.rb --help
***************
*** 86,94 ****
  for more details.

  If you want to use the OBDA (Open Bio Database Access) to obtain database
! entries, copy a sample config file

!   etc/bioinformatics/seqdatabase.ini

  to
--- 118,134 ----
  for more details.

+ --- RubyGems
+ 
+ If you are using RubyGems, just type
+ 
+   % gems install bio
+ 
+ 
+ == SETUP

  If you want to use the OBDA (Open Bio Database Access) to obtain database
! entries, copy a sample configtation file in the BioRuby distribution

!   bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini

  to
***************
*** 106,131 ****
  == USAGE

! You can load all BioRuby classes just by require 'bio' and all the
! BioRuby classes are defined under the module Bio for the name space.
! See the documentation for each class.

    #!/usr/bin/env ruby
    require 'bio'

  == LICENCE

! GPL for applications, LGPL for libraries.  Note that, install.rb
! included in the BioRuby package comes from [RAA:setup] by Minero Aoki.

- == AUTHORS

! * KATAYAMA Toshiaki <k at bioruby.org>, project leader
! * Yoshinori K. Okuji <okuji at enbug.org>
! * Mitsuteru C. Nakao <n at bioruby.org>
! * KAWASHIMA Shuichi <s at bioruby.org>
! * GOTO Naohisa <ng at bioruby.org>

!   * and many others on the Internet...

--- 146,182 ----
  == USAGE

! You can load all BioRuby classes just by requiring 'bio.rb'.  All the
! BioRuby classes and modules are located under the module name 'Bio' to
! separate the name space.

    #!/usr/bin/env ruby
    require 'bio'

+ Also read other documentations in the 'doc' directory.
+ 
+   bioruby-x.x.x/doc/
+ 
+ --- RubyGems
+ 
+ In RubyGems, you need to load 'rubygems' library before using 'bio'.
+ 
+   #!/usr/bin/env ruby
+   require 'rubygems'
+   require_gem 'bio'

  == LICENCE

! BioRuby can be freely distributed under the GNU LGPL licence.

+ Note that, install.rb included in the BioRuby package comes from
+ [RAA:setup] developed by Minero Aoki, and modified by Moses Hohman.

! == CONTACT

! Current staffs of the BioRuby project can be reached by sending e-mail
! to <staff at bioruby.org>.
! 
! 
! =end