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Commits on Mar 18, 2015
  1. @ngoto

    try to use bio-old-biofetch-emulator gem

    ngoto authored
     * bin/br_biofetch.rb: try to use bio-old-biofetch-emulator gem.
       Without bio-old-biofetch-emulator, the program exits with error
       message when default BioRuby BioFetch server is specified.
  2. @ngoto
  3. @ngoto

    Revert e29fc5f

    ngoto authored
     * bin/br_biofetch.rb: revert e29fc5f
       because the old deprecated bioruby biofetch server can be emulated
       by bio-old-biofetch-emulator gem package.
Commits on Nov 11, 2014
  1. @ngoto

    remove unused $Id:$ line

    ngoto authored
  2. @ngoto

    Change default server to EBI Dbfetch server; remove BioRuby BioFetch …

    ngoto authored
    …server
    
     * Change default server to EBI Dbfetch server.
     * The BioRuby BioFetch server is removed. When "-r" option (force to use
       BioRuby server) is specified, warning message is shown, and the program
       exits with code 1 (abnormal exit).
     * Usage message is also changed.
Commits on Dec 24, 2009
  1. @ngoto
Commits on Jan 29, 2009
  1. @ngoto
Commits on Jul 10, 2008
  1. @ngoto

    When creating flatfile index, "env LC_ALL=C" is added to avoid locale…

    ngoto authored
    … issue
    
    * In lib/bio/io/flatfile/indexer.rb and lib/bio/io/flatfile/index.rb,
      to fix a bug that invalid index is generated when LANG=en_US.UTF-8,
      when executing "/usr/bin/sort" (or sort program given by user),
      doing "/usr/bin/env LC_ALL=C" by default to avoid effects of locales.
      Note that users can specify path of env program and arguments with options.
    * In bin/br_bioflat.rb, added new option --env=/path/to/env and
      --env-arg=XXX (e.g. LC_ALL=C), corresponding to above changes.
      In addition, fixed a bug --format=XXX option was ignored.
Commits on Jul 26, 2007
  1. @ktym

    * removed unnecessary lines which are temporally added during several

    ktym authored
      attempts to integrate Rails in shell (but now it is supported by
      shell/irb.rb and shell/web.rb)
  2. @ktym
Commits on Apr 5, 2007
  1. @trevor
Commits on Dec 24, 2006
  1. @ktym

    * updated for version 1.1.0 (need to use 'gem install bio --no-wrappe…

    ktym authored
    …rs' to
    
      avoid modification of bin/* files by RubyGems)
  2. @ktym
Commits on Jul 25, 2006
  1. @ktym
Commits on Feb 27, 2006
  1. @ktym

    * temporal cleanup

    ktym authored
  2. @ktym

    * history file with timestamp

    ktym authored
    * rails server workaround (may not yet complete with open3)
Commits on Feb 22, 2006
  1. @ngoto

    changed STDERR to $stderr

    ngoto authored
Commits on Feb 14, 2006
  1. @ktym

    * Bio::Shell::Ghost#load/save methods are renamed to

    ktym authored
      load_session/save_session respectively to avoid method
      name collision with Kernel#load
Commits on Feb 9, 2006
  1. @ktym

    * fixed to run without argument. if argument is not given, current di…

    ktym authored
    …rectory
    
      will be used to save session
  2. @ktym

    * license is changed to Ruby's

    ktym authored
  3. @ktym

    * license changed

    ktym authored
    * if argument is given,
      1. arg == dir  : chdir to the specified working directory at start up or
      2. arg == file : run the fille as a bioruby shell script or
      3. arg == str  : create the new directory to work on
Commits on Dec 7, 2005
  1. @ktym

    * lib/bioruby.rb is added for easy bioruby script startup after the d…

    ktym authored
    …iscussion
    
      with Tanka-san (.bioruby/script.rb will use this)
    * access.rb plugin is moved under the plugin directory as a entry.rb
    * Core is changed to Ghost :)
Commits on Nov 28, 2005
  1. @ktym

    * open/close is renamed to load/save

    ktym authored
    * other method names are unified in core.rb for clean up
Commits on Nov 27, 2005
  1. @ktym

    * Bio::Shell::Core::Config and Bio::Shell::Core::Cache are changed to

    ktym authored
      @config and @cache which are initialized in Bio::Shell.setup as a Hash
      and have accessors (Bio::Shell.config, Bio::Shell.cache).
Commits on Nov 24, 2005
  1. @ktym

    * global variable $bioruby_config and $bioruby_cache are removed (cha…

    ktym authored
    …nged to
    
      use Bio::Shell::Core::Config & Cache, which have accessor methods like
      Bio::Shell.config(param, value), Bio::Shell.cache(param, value))
Commits on Nov 14, 2005
  1. @ktym

    * fixed typo s/lisence/license/

    ktym authored
Commits on Nov 6, 2005
  1. @ktym
Commits on Nov 5, 2005
  1. @ktym

    * converted to RDoc

    ktym authored
    * opening, closing methods are renamed to open and close
Commits on Oct 27, 2005
  1. Documenting bioruby shell

    Pjotr Prins authored
Commits on Sep 24, 2005
  1. @ktym

    * load/save history is suppressed when readline isn't available

    ktym authored
    * $bioruby_cache variable is introduced for non persistent configuration
Commits on Sep 23, 2005
  1. @ktym
Commits on Jul 11, 2005
  1. @ktym
Commits on Jan 6, 2005
  1. @ktym

    * Bio::Reference#abstract method is renamed to Bio::Reference#rd as it

    ktym authored
      produces MEDLINE abstract in RD format (part of the Ruby's documentation        format).
Commits on Jul 27, 2004
  1. @ktym
Commits on Feb 5, 2004
  1. @ktym
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