bio-shell 0.0.0

data/lib/bioruby.rb

@@ -0,0 +1,34 @@
+#
+# = bioruby.rb - Loading all BioRuby modules and setup for shell programming
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: bioruby.rb,v 1.1 2005/12/07 05:12:06 k Exp $
+#
+#--
+#
+#  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 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+require 'bio/shell'
+
+include Bio::Shell
+
+Bio::Shell.setup
+

metadata

@@ -0,0 +1,165 @@
+--- !ruby/object:Gem::Specification
+name: bio-shell
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- BioRuby project
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2017-09-15 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.1
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3'
+description: BioRuby Shell is a command-line based interacitve analysis enviroment
+  for BioRuby open source bioinformatics library.
+email:
+- staff@bioruby.org
+executables:
+- bioruby
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- BSDL
+- COPYING
+- COPYING.ja
+- Gemfile
+- LEGAL
+- README.md
+- Rakefile
+- bin/bioruby
+- bio-shell.gemspec
+- lib/bio/shell.rb
+- lib/bio/shell/core.rb
+- lib/bio/shell/demo.rb
+- lib/bio/shell/interface.rb
+- lib/bio/shell/irb.rb
+- lib/bio/shell/object.rb
+- lib/bio/shell/plugin/blast.rb
+- lib/bio/shell/plugin/codon.rb
+- lib/bio/shell/plugin/das.rb
+- lib/bio/shell/plugin/emboss.rb
+- lib/bio/shell/plugin/entry.rb
+- lib/bio/shell/plugin/flatfile.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/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
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
+- lib/bio/shell/script.rb
+- lib/bio/shell/setup.rb
+- lib/bio/shell/version.rb
+- lib/bio/shell/web.rb
+- lib/bioruby.rb
+homepage: https://github.com/bioruby/bioruby-shell
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.11
+signing_key: 
+specification_version: 4
+summary: 'BioRuby Shell: interactive analysis environment for BioRuby'
+test_files: []