[BioRuby] BioRuby Shell Rails Generator Bug ?

Raoul Jean Pierre Bonnal raoul.bonnal at itb.cnr.it
Tue Jan 29 10:40:31 UTC 2008

[root at Graco febo]# gem install bio
Updating metadata for 30 gems from http://gems.rubyforge.org
Successfully installed bio-1.2.1
1 gem installed
[febo at Graco Projects]$ bioruby -r testrb
Creating directory (/home/febo/Work/Projects/testrb/shell/session) ...
Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ...
Creating directory (/home/febo/Work/Projects/testrb/data) ... done
Installing Rails application for BioRuby shell ... 
a lot of create ....

Installing Rails plugin for BioRuby shell ... 
Couldn't find 'bioruby' generator
Then Rails starts.

So digging into the installation tree I
found  /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/

and taking as example uniprot plugins

[root at Graco febo]#
ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/
[root at Graco febo]#
mkdir /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby
[root at Graco febo]#
mv /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby
[root at Graco febo]#
ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/
totale 1
drwxr-xr-x 3 root root 1024 2008-01-29 11:37 bioruby/

[febo at Graco Projects]$ bioruby -r testrb
Creating directory (/home/febo/Work/Projects/testrb/shell/session) ...
Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ...
Creating directory (/home/febo/Work/Projects/testrb/data) ... done
Installing Rails application for BioRuby shell ... 
      create  app/controllers
      create  app/helpers
      create  app/models
      create  app/views/layouts
      create  config/environments
      create  config/initializers
      create  db
      create  doc
      create  lib
      create  lib/tasks
      create  log
      create  public/images
      create  public/javascripts
      create  public/stylesheets
      create  script/performance
      create  script/process
      create  test/fixtures
      create  test/functional
      create  test/integration
      create  test/mocks/development
      create  test/mocks/test
      create  test/unit
      create  vendor
      create  vendor/plugins
      create  tmp/sessions
      create  tmp/sockets
      create  tmp/cache
      create  tmp/pids
      create  Rakefile
      create  README
      create  app/controllers/application.rb
      create  app/helpers/application_helper.rb
      create  test/test_helper.rb
      create  config/database.yml
      create  config/routes.rb
      create  public/.htaccess
      create  config/initializers/inflections.rb
      create  config/initializers/mime_types.rb
      create  config/boot.rb
      create  config/environment.rb
      create  config/environments/production.rb
      create  config/environments/development.rb
      create  config/environments/test.rb
      create  script/about
      create  script/console
      create  script/destroy
      create  script/generate
      create  script/performance/benchmarker
      create  script/performance/profiler
      create  script/performance/request
      create  script/process/reaper
      create  script/process/spawner
      create  script/process/inspector
      create  script/runner
      create  script/server
      create  script/plugin
      create  public/dispatch.rb
      create  public/dispatch.cgi
      create  public/dispatch.fcgi
      create  public/404.html
      create  public/422.html
      create  public/500.html
      create  public/index.html
      create  public/favicon.ico
      create  public/robots.txt
      create  public/images/rails.png
      create  public/javascripts/prototype.js
      create  public/javascripts/effects.js
      create  public/javascripts/dragdrop.js
      create  public/javascripts/controls.js
      create  public/javascripts/application.js
      create  doc/README_FOR_APP
      create  log/server.log
      create  log/production.log
      create  log/development.log
      create  log/test.log
Installing Rails plugin for BioRuby shell ... 
      exists  app/controllers
      exists  app/helpers
      create  app/views/bioruby
      exists  app/views/layouts
      create  public/images/bioruby
      exists  public/stylesheets
      create  app/controllers/bioruby_controller.rb
      create  app/helpers/bioruby_helper.rb
      create  app/views/bioruby/_methods.rhtml
      create  app/views/bioruby/_classes.rhtml
      create  app/views/bioruby/_modules.rhtml
      create  app/views/bioruby/_log.rhtml
      create  app/views/bioruby/_variables.rhtml
      create  app/views/bioruby/commands.rhtml
      create  app/views/bioruby/history.rhtml
      create  app/views/bioruby/index.rhtml
      create  app/views/layouts/bioruby.rhtml
      create  public/images/bioruby/spinner.gif
      create  public/images/bioruby/gem.png
      create  public/images/bioruby/link.gif
      create  public/images/bioruby/bg.gif
      create  public/stylesheets/bioruby.css

>>>  open http://localhost:3000/bioruby

(You can change the port number by adding "-- -p 4000" option)

. . . B i o R u b y   i n   t h e   s h e l l . . .

  Version : BioRuby 1.2.1 / Ruby 1.8.6

=> Booting WEBrick...
=> Rails application started on
=> Ctrl-C to shutdown server; call with --help for options
[2008-01-29 11:37:51] INFO  WEBrick 1.3.1
[2008-01-29 11:37:51] INFO  ruby 1.8.6 (2007-03-13) [i586-linux-gnu]
[2008-01-29 11:37:51] INFO  WEBrick::HTTPServer#start: pid=9210



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