quorum 0.1.0

data/.gitignore

@@ -0,0 +1,10 @@
+.bundle/
+log/*.log
+pkg/
+spec/dummy/db/*.sqlite3
+spec/dummy/db/migrate/
+spec/dummy/log/*.log
+spec/dummy/tmp/
+spec/dummy/config/database.yml
+spec/dummy/quorum/log/*
+spec/dummy/quorum/tmp/*

data/.rspec

@@ -0,0 +1 @@
+--colour

data/Gemfile

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+source "http://rubygems.org"
+
+# Declare your gem's dependencies in quorum.gemspec.
+# Bundler will treat runtime dependencies like base dependencies, and
+# development dependencies will be added by default to the :development group.
+gemspec
+
+# Declare any dependencies that are still in development here instead of in
+# your gemspec. These might include edge Rails or gems from your path or
+# Git. Remember to move these dependencies to your gemspec before releasing
+# your gem to rubygems.org.
+
+# To use debugger
+# gem 'ruby-debug19', :require => 'ruby-debug'
+

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    quorum (0.1.0)
+      bio-blastxmlparser (~> 1.0.1)
+      jquery-rails
+      net-ssh (~> 2.2.1)
+      rails (~> 3.1.0)
+      resque (~> 1.19.0)
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    actionmailer (3.1.0)
+      actionpack (= 3.1.0)
+      mail (~> 2.3.0)
+    actionpack (3.1.0)
+      activemodel (= 3.1.0)
+      activesupport (= 3.1.0)
+      builder (~> 3.0.0)
+      erubis (~> 2.7.0)
+      i18n (~> 0.6)
+      rack (~> 1.3.2)
+      rack-cache (~> 1.0.3)
+      rack-mount (~> 0.8.2)
+      rack-test (~> 0.6.1)
+      sprockets (~> 2.0.0)
+    activemodel (3.1.0)
+      activesupport (= 3.1.0)
+      bcrypt-ruby (~> 3.0.0)
+      builder (~> 3.0.0)
+      i18n (~> 0.6)
+    activerecord (3.1.0)
+      activemodel (= 3.1.0)
+      activesupport (= 3.1.0)
+      arel (~> 2.2.1)
+      tzinfo (~> 0.3.29)
+    activeresource (3.1.0)
+      activemodel (= 3.1.0)
+      activesupport (= 3.1.0)
+    activesupport (3.1.0)
+      multi_json (~> 1.0)
+    arel (2.2.1)
+    bcrypt-ruby (3.0.0)
+    bio-blastxmlparser (1.0.1)
+      bio-logger (>= 1.0.0)
+      nokogiri (>= 1.5.0)
+    bio-logger (1.0.0)
+      log4r (>= 1.1.9)
+    builder (3.0.0)
+    capybara (1.1.1)
+      mime-types (>= 1.16)
+      nokogiri (>= 1.3.3)
+      rack (>= 1.0.0)
+      rack-test (>= 0.5.4)
+      selenium-webdriver (~> 2.0)
+      xpath (~> 0.1.4)
+    childprocess (0.2.2)
+      ffi (~> 1.0.6)
+    database_cleaner (0.6.7)
+    diff-lcs (1.1.3)
+    erubis (2.7.0)
+    factory_girl (2.1.0)
+    factory_girl_rails (1.2.0)
+      factory_girl (~> 2.1.0)
+      railties (>= 3.0.0)
+    ffi (1.0.9)
+    hike (1.2.1)
+    i18n (0.6.0)
+    jquery-rails (1.0.16)
+      railties (~> 3.0)
+      thor (~> 0.14)
+    json_pure (1.5.4)
+      spruz (~> 0.2.8)
+    log4r (1.1.9)
+    mail (2.3.0)
+      i18n (>= 0.4.0)
+      mime-types (~> 1.16)
+      treetop (~> 1.4.8)
+    mime-types (1.16)
+    multi_json (1.0.3)
+    mysql2 (0.3.7)
+    net-ssh (2.2.1)
+    nokogiri (1.5.0)
+    polyglot (0.3.2)
+    rack (1.3.2)
+    rack-cache (1.0.3)
+      rack (>= 0.4)
+    rack-mount (0.8.3)
+      rack (>= 1.0.0)
+    rack-protection (1.1.4)
+      rack
+    rack-ssl (1.3.2)
+      rack
+    rack-test (0.6.1)
+      rack (>= 1.0)
+    rails (3.1.0)
+      actionmailer (= 3.1.0)
+      actionpack (= 3.1.0)
+      activerecord (= 3.1.0)
+      activeresource (= 3.1.0)
+      activesupport (= 3.1.0)
+      bundler (~> 1.0)
+      railties (= 3.1.0)
+    railties (3.1.0)
+      actionpack (= 3.1.0)
+      activesupport (= 3.1.0)
+      rack-ssl (~> 1.3.2)
+      rake (>= 0.8.7)
+      rdoc (~> 3.4)
+      thor (~> 0.14.6)
+    rake (0.9.2)
+    rdoc (3.9.4)
+    redis (2.2.2)
+    redis-namespace (1.0.3)
+      redis (< 3.0.0)
+    resque (1.19.0)
+      multi_json (~> 1.0)
+      redis-namespace (~> 1.0.2)
+      sinatra (>= 0.9.2)
+      vegas (~> 0.1.2)
+    rspec (2.6.0)
+      rspec-core (~> 2.6.0)
+      rspec-expectations (~> 2.6.0)
+      rspec-mocks (~> 2.6.0)
+    rspec-core (2.6.4)
+    rspec-expectations (2.6.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.6.0)
+    rspec-rails (2.6.1)
+      actionpack (~> 3.0)
+      activesupport (~> 3.0)
+      railties (~> 3.0)
+      rspec (~> 2.6.0)
+    rubyzip (0.9.4)
+    selenium-webdriver (2.5.0)
+      childprocess (>= 0.2.1)
+      ffi (>= 1.0.7)
+      json_pure
+      rubyzip
+    sinatra (1.3.0)
+      rack (~> 1.3)
+      rack-protection (~> 1.1)
+      tilt (~> 1.3)
+    sprockets (2.0.0)
+      hike (~> 1.2)
+      rack (~> 1.0)
+      tilt (~> 1.1, != 1.3.0)
+    spruz (0.2.13)
+    thor (0.14.6)
+    tilt (1.3.3)
+    treetop (1.4.10)
+      polyglot
+      polyglot (>= 0.3.1)
+    tzinfo (0.3.30)
+    vegas (0.1.8)
+      rack (>= 1.0.0)
+    xpath (0.1.4)
+      nokogiri (~> 1.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  capybara
+  database_cleaner
+  factory_girl_rails (~> 1.2.0)
+  mysql2
+  quorum!
+  rspec-rails (~> 2.6)

data/MIT-LICENSE

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+Copyright NCGR
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= Quorum
+
+A flexible bioinformatics search tool.
+
+Quorum is a Rails 3.1 mountable engine that supports the following 
+bioinformatics search tools.
+
+* NCBI Blast+ (http://blast.ncbi.nlm.nih.gov)
+
+Dependencies:
+
+* Rails >= 3.1.0
+* Redis >= 0.900 for Resque (https://github.com/defunkt/resque)
+* NCBI Blast+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
+* Emboss (http://emboss.sourceforge.net/)
+
+See the gem in action.
+
+http://medplants.ncgr.org/quorum/jobs/new
+
+== Installation
+
+Use the latest stable Rails release with Quorum.
+
+  gem install quorum
+
+After you install Quorum and add it to your Gemfile, run the generator.
+
+  rails generate quorum:install
+
+The generator will create a directory in your application's root path
+
+  quorum/  
+
+as well as the necessary config files to run and customize Quorum. You
+MUST customize "config/quorum_settings.yml" before using Quorum. See Remote
+Machine Setup below if you choose to execute Quorum remotely.
+
+Migrate the database.
+
+  rake quorum:install:migrations
+  rake db:migrate
+
+== Getting Started
+
+=== NCBI Blast+ Setup
+
+Build your NCBI Blast+ database(s) using the rake task below.
+
+  rake quorum:blastdb:build
+
+Arguments:
+
+* DIR= - path to {.tgz, .tar.gz, .tbz, .tar.bz2} files containing raw data.
+  Separate multiple directories with a colon (:).
+
+  DIR=/path/to/dir:/path/to/another/dir
+
+* TYPE= - type of Blast database to build {both, prot, nucl}. Defaults to
+  both.
+
+* PROT_FILE_NAME= - name of the file containing protein data. Defaults to
+  peptides.fa.
+
+* NUCL_FILE_NAME= - name of the file containing nucleotide data. Defaults
+  to contigs.fa.
+
+* REBUILD_DB= - removes existing blast database(s) before building {true or
+  false}. Defaults to false. 
+
+* EMPTY= - skip makeblastdb and create necessary directories {true or false}.
+  Defaults to false. Set this argument to true if you wish to create your own
+  Blast database(s).
+
+Example:
+
+  rake quorum:blastdb:build DIR=/path/to/dir:/path/to/another/dir TYPE=nucl \
+  NUCL_FILE_NAME=my_contigs.fa REBUILD_DB=true
+
+Empty example:
+
+  rake quorum:blastdb:build EMPTY=true
+
+For a full list of supported arguments.
+
+  rake -D
+
+Don't forget to update "config/quorum_settings.yml" with your newly created 
+database(s).
+
+=== Remote Machine Setup -- Recommended for Production Use
+
+Follow the steps below to execute Quorum remotely via Net::SSH.
+
+* Ensure your ActiveRecord Database adapter in "config/database.yml" is set to 
+  *any* supported adapter other than sqlite3.
+
+* Ensure your database host is set and accessible via the remote machine(s).
+
+* Ensure you have supplied the necessary information in 
+  "config/quorum_settings.yml" to execute Quorum remotely.
+
+  remote: true
+  ssh_host: remote.machine.org
+  ssh_user: remote_user
+  
+Net::SSH.start() optional params (http://net-ssh.github.com/ssh/v2/api/index.html)
+
+  ssh_options:
+    password: "secret"
+    port: 8888
+
+* Tar and compress quorum.
+
+  tar -czvf quorum.tar.gz quorum/
+
+* Copy the newly created tarball to the remote machine.
+
+  scp quorum.tar.gz <username>@<host>:/path/to/install
+
+* Expand the tarball on the remote machine.
+
+  ssh <username>@<host>        
+
+  tar -xzvf quorum.tar.gz
+
+* Ensure Quorum script dependencies are added to the remote machine's PATH. 
+  If the remote machine doesn't have a .bashrc file, create one.
+
+  touch /path/to/.bashrc
+
+and add script dependencies to PATH.
+
+  echo "export PATH=/path/to/dependencies:$PATH" >> /path/to/.bashrc
+
+=== Customize Quorum's Views and Styles
+
+To override Quorum's default views, run the generator.
+
+  rails generate quorum:views
+
+A copy of Quorum's views can be found in your application under 
+"app/views/quorum/". 
+
+To override Quorum's default styles, run the generator.
+
+  rails generate quorum:styles
+
+A copy of Quorum's styles can be found in your application under
+"app/assets/stylesheets/quorum/". If your application has existing styles,
+it's a good idea to remove
+
+  *= require_tree .
+
+in "app/assets/stylesheets/application.css" and require your stylesheets 
+individually.
+
+Don't plan on supporting all of Quorum's alogrithms? Override Quorum's views 
+and comment out any unwanted algorithms in "app/views/quorum/jobs/new.html.erb" 
+and "app/views/quorum/jobs/show.html.erb".
+
+For example:
+
+Remove Blastp in "app/views/quorum/jobs/new.html.erb"
+
+  <!-- Search Algorithms -->
+  <!-- Comment out an alorithm below to remove it from the form. -->
+
+  <!-- blastn -->
+  <%= render :partial => "blastn_form", :locals => { 
+    :f => f, :blast_dbs => @blast_dbs } %>
+
+  <!-- blastx -->
+  <%= render :partial => "blastx_form", :locals => { 
+    :f => f, :blast_dbs => @blast_dbs } %>
+
+  <!-- tblastn -->
+  <%= render :partial => "tblastn_form", :locals => { 
+    :f => f, :blast_dbs => @blast_dbs } %>
+
+  <!-- blastp -->
+  <% render :partial => "blastp_form", :locals => { 
+    :f => f, :blast_dbs => @blast_dbs } %>
+
+  <!-- End Search Algorithms -->
+
+Remove Blastp in "app/views/quorum/jobs/show.html.erb"
+
+  <div id="tabs">
+    <ul>
+      <li><a href="#tabs-1">Blastn</a></li>
+      <li><a href="#tabs-2">Blastx</a></li>
+      <li><a href="#tabs-3">Tblastn</a></li>
+      <!--
+      <li><a href="#tabs-4">Blastp</a></li>
+      -->
+    </ul>
+
+    <!-- Search results per algorithm -->
+    <div id="tabs-1">
+      <h2>Blastn</h2>
+      <div id="blastn-results">
+        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+      </div>
+    </div>
+
+    <div id="tabs-2">
+      <h2>Blastx</h2>
+      <div id="blastx-results">
+        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+      </div>
+    </div>
+
+    <div id="tabs-3">
+      <h2>Tblastn</h2>
+      <div id="tblastn-results">
+        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+      </div>
+    </div>
+
+    <!--
+    <div id="tabs-4">
+      <h2>Blastp</h2>
+      <div id="blastp-results">
+        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+      </div>
+    </div>
+    -->
+  </div>
+
+=== Redis
+
+For detailed Redis installation instructions, follow the links below.
+
+* Redis (http://redis.io/)
+* Resque (https://github.com/defunkt/resque)
+
+=== Resque
+
+Quorum provides a simple Rails environment rake task for spawning Resque 
+workers. To customize Resque workers by adding monitoring etc., follow 
+the link below.
+
+* Resque (https://github.com/defunkt/resque)
+
+<b>Resque Web Interface</b>
+
+Quorum mounts Resque's web interface by default via 
+
+  mount Resque::Server.new, :at => "/quorum/resque"
+
+in "config/routes.rb". The line above is fine for development, however, in
+production it's best to grant authenticated users access to "/quorum/resque".
+
+HTTP Basic Example:
+"config/initializers/resque_http_auth.rb"
+
+  Resque::Server.use(Rack::Auth::Basic) do |user, password|
+    user     == "resque"
+    password == "secret"
+  end
+
+Devise Example:
+"config/routes.rb"
+
+  authenticate :user do
+    mount Resque::Server.new, :at => "/quorum/resque"
+  end
+
+Devise plus Declarative Authorization Example:
+"config/routes.rb"
+
+  # Only superusers can access Resque's web interface.
+  resque_constraint = lambda do |request|
+    request.env["warden"].authenticate? && 
+    request.env["warden"].user.role_symbols.include?(:superuser)
+  end 
+
+  constraints resque_constraint do
+    mount Resque::Server.new, :at => "/quorum/resque"
+  end
+
+=== I18n
+
+To customize Quorum flash messages, edit "config/locales/quorum.en.yml".
+
+== Additional Information
+
+=== Bugs?
+
+https://github.com/ncgr/quorum/issues
+
+=== Contributing
+
+* Fork Quorum
+* Create a topic branch <code>git checkout -b my_branch</code>
+* Push to your branch <code>git push origin my_branch</code>
+* Create a pull request from your branch
+* Find your name added to the README under Contributors
+
+=== TODO
+
+* Add GFF3 annotations to detailed Blast reports
+* Add link to download Blast hit sequence in detailed report
+* Support Hmmer3
+
+=== Maintained By
+
+* Ken Seal (https://github.com/hunzinker)
+
+=== Contributors
+
+* John Crow (https://github.com/crowja)
+* Andrew Farmer
+
+== License
+
+MIT License. Copyright NCGR http://ncgr.org/

data/Rakefile

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+#!/usr/bin/env rake
+begin
+  require 'bundler/setup'
+rescue LoadError
+  puts 'You must `gem install bundler` and `bundle install` to run rake tasks'
+end
+begin
+  require 'rdoc/task'
+rescue LoadError
+  require 'rdoc/rdoc'
+  require 'rake/rdoctask'
+  RDoc::Task = Rake::RDocTask
+end
+
+RDoc::Task.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'Quorum'
+  rdoc.options << '--line-numbers'
+  rdoc.rdoc_files.include('README.rdoc')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+APP_RAKEFILE = File.expand_path("../spec/dummy/Rakefile", __FILE__)
+load 'rails/tasks/engine.rake'
+
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec)
+task :default => :spec
+
+Bundler::GemHelper.install_tasks
+

data/app/assets/javascripts/quorum/application.js

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+// This is a manifest file that'll be compiled into including all the files listed below.
+// Add new JavaScript/Coffee code in separate files in this directory and they'll automatically
+// be included in the compiled file accessible from http://example.com/assets/application.js
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// the compiled file.
+//
+//= require jquery
+//= require jquery_ujs
+//= require jquery-ui
+//= require underscore-min
+//= require jquery.tipsy
+//= require_tree .
+