quorum 0.1.0

data/db/migrate/20111031204518_create_jobs.rb

@@ -0,0 +1,12 @@
+class CreateJobs < ActiveRecord::Migration
+  def change
+    create_table :quorum_jobs do |t|
+      t.text :sequence, :null => false
+      t.text :na_sequence, :null => true
+      t.text :aa_sequence, :null => true
+      t.string :sequence_hash, :nul => true
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204701_create_blastn_jobs.rb

@@ -0,0 +1,19 @@
+class CreateBlastnJobs < ActiveRecord::Migration
+  def change
+    create_table :quorum_blastn_jobs do |t|
+      t.string :expectation
+      t.integer :max_score
+      t.integer :min_bit_score
+      t.boolean :filter
+      t.boolean :gapped_alignments
+      t.integer :gap_opening_penalty
+      t.integer :gap_extension_penalty
+      t.text :blast_dbs
+      t.boolean :queue
+
+      t.references :job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204719_create_blastx_jobs.rb

@@ -0,0 +1,19 @@
+class CreateBlastxJobs < ActiveRecord::Migration
+  def change
+    create_table :quorum_blastx_jobs do |t|
+      t.string :expectation
+      t.integer :max_score
+      t.integer :min_bit_score
+      t.boolean :filter
+      t.boolean :gapped_alignments
+      t.integer :gap_opening_penalty
+      t.integer :gap_extension_penalty
+      t.text :blast_dbs
+      t.boolean :queue
+
+      t.references :job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204733_create_blastp_jobs.rb

@@ -0,0 +1,19 @@
+class CreateBlastpJobs < ActiveRecord::Migration
+  def change
+    create_table :quorum_blastp_jobs do |t|
+      t.string :expectation
+      t.integer :max_score
+      t.integer :min_bit_score
+      t.boolean :filter
+      t.boolean :gapped_alignments
+      t.integer :gap_opening_penalty
+      t.integer :gap_extension_penalty
+      t.text :blast_dbs
+      t.boolean :queue
+
+      t.references :job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204754_create_tblastn_jobs.rb

@@ -0,0 +1,19 @@
+class CreateTblastnJobs < ActiveRecord::Migration
+  def change
+    create_table :quorum_tblastn_jobs do |t|
+      t.string :expectation
+      t.integer :max_score
+      t.integer :min_bit_score
+      t.boolean :filter
+      t.boolean :gapped_alignments
+      t.integer :gap_opening_penalty
+      t.integer :gap_extension_penalty
+      t.text :blast_dbs
+      t.boolean :queue
+
+      t.references :job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204846_create_blastn_job_reports.rb

@@ -0,0 +1,34 @@
+class CreateBlastnJobReports < ActiveRecord::Migration
+  def change
+    create_table :quorum_blastn_job_reports do |t|
+      t.string :query
+      t.integer :query_len
+      t.string :hit_id
+      t.string :hit_def
+      t.string :hit_accession
+      t.integer :hit_len
+      t.integer :hsp_num
+      t.string :hsp_group
+      t.integer :bit_score
+      t.integer :score
+      t.string :evalue
+      t.integer :query_from
+      t.integer :query_to
+      t.integer :hit_from
+      t.integer :hit_to
+      t.string :query_frame
+      t.string :hit_frame
+      t.integer :identity
+      t.integer :positive
+      t.integer :align_len
+      t.text :qseq
+      t.text :hseq
+      t.text :midline
+      t.boolean :results
+
+      t.references :blastn_job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204903_create_blastx_job_reports.rb

@@ -0,0 +1,34 @@
+class CreateBlastxJobReports < ActiveRecord::Migration
+  def change
+    create_table :quorum_blastx_job_reports do |t|
+      t.string :query
+      t.integer :query_len
+      t.string :hit_id
+      t.string :hit_def
+      t.string :hit_accession
+      t.integer :hit_len
+      t.integer :hsp_num
+      t.string :hsp_group
+      t.integer :bit_score
+      t.integer :score
+      t.string :evalue
+      t.integer :query_from
+      t.integer :query_to
+      t.integer :hit_from
+      t.integer :hit_to
+      t.string :query_frame
+      t.string :hit_frame
+      t.integer :identity
+      t.integer :positive
+      t.integer :align_len
+      t.text :qseq
+      t.text :hseq
+      t.text :midline
+      t.boolean :results
+
+      t.references :blastx_job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204922_create_blastp_job_reports.rb

@@ -0,0 +1,34 @@
+class CreateBlastpJobReports < ActiveRecord::Migration
+  def change
+    create_table :quorum_blastp_job_reports do |t|
+      t.string :query
+      t.integer :query_len
+      t.string :hit_id
+      t.string :hit_def
+      t.string :hit_accession
+      t.integer :hit_len
+      t.integer :hsp_num
+      t.string :hsp_group
+      t.integer :bit_score
+      t.integer :score
+      t.string :evalue
+      t.integer :query_from
+      t.integer :query_to
+      t.integer :hit_from
+      t.integer :hit_to
+      t.string :query_frame
+      t.string :hit_frame
+      t.integer :identity
+      t.integer :positive
+      t.integer :align_len
+      t.text :qseq
+      t.text :hseq
+      t.text :midline
+      t.boolean :results
+
+      t.references :blastp_job
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20111031204941_create_tblastn_job_reports.rb

@@ -0,0 +1,34 @@
+class CreateTblastnJobReports < ActiveRecord::Migration
+  def change
+    create_table :quorum_tblastn_job_reports do |t|
+      t.string :query
+      t.integer :query_len
+      t.string :hit_id
+      t.string :hit_def
+      t.string :hit_accession
+      t.integer :hit_len
+      t.integer :hsp_num
+      t.string :hsp_group
+      t.integer :bit_score
+      t.integer :score
+      t.string :evalue
+      t.integer :query_from
+      t.integer :query_to
+      t.integer :hit_from
+      t.integer :hit_to
+      t.string :query_frame
+      t.string :hit_frame
+      t.integer :identity
+      t.integer :positive
+      t.integer :align_len
+      t.text :qseq
+      t.text :hseq
+      t.text :midline
+      t.boolean :results
+
+      t.references :tblastn_job
+
+      t.timestamps
+    end
+  end
+end

data/lib/generators/quorum/install_generator.rb

@@ -0,0 +1,68 @@
+module Quorum
+  module Generators
+    class InstallGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../templates", __FILE__)
+
+      desc "Creates Quorum initializer, settings and " <<
+           "search tool files."
+
+      DEPENDENCIES = ["makeblastdb", "seqret"]
+
+      def copy_initializer
+        template "quorum_initializer.rb", 
+          "config/initializers/quorum_initializer.rb"
+        template "quorum_settings.yml", "config/quorum_settings.yml"
+        template "search", "quorum/bin/search"
+        template "trollop.rb", "quorum/lib/trollop.rb"
+        template "logger.rb", "quorum/lib/logger.rb"
+        template "blast.rb", "quorum/lib/search_tools/blast.rb"
+      end
+
+      def copy_locale
+        copy_file "../../../config/locales/en.yml", "config/locales/quorum.en.yml"
+      end
+
+      def change_file_permissions
+        f = File.new("quorum/bin/search", "r")
+        f.chmod(0755)
+      end
+
+      def create_quorum_tmp_dir
+        Dir.mkdir("quorum/tmp") unless File.directory?("quorum/tmp")
+      end
+
+      def create_quorum_log_dir
+        Dir.mkdir("quorum/log") unless File.directory?("quorum/log")
+      end
+
+      def add_mount_engine
+        route %Q(mount Quorum::Engine => "/quorum")
+      end
+
+      def add_resque_mount_engine
+        route %Q(mount Resque::Server.new, :at => "/quorum/resque")
+      end
+
+      def check_dependencies
+        puts ""
+        puts "Checking Quorum system dependencies..."
+        messages = []
+        DEPENDENCIES.each do |b|
+          system("which #{b} > /dev/null 2>&1")
+          if $?.exitstatus > 0
+            messages << "Please add `#{b}` to your PATH."
+          end
+        end
+        unless messages.empty?
+          puts "*** Warning: Quorum system dependencies not found ***"
+          messages.each { |m| puts m }
+          puts ""
+        end
+      end
+
+      def show_readme
+        readme "README"
+      end
+    end
+  end
+end

data/lib/generators/quorum/styles_generator.rb

@@ -0,0 +1,18 @@
+module Quorum
+  module Generators
+    class StylesGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../../../app/assets/stylesheets", __FILE__)
+      desc "Copy quorum stylesheets to your application."
+
+      STYLE_DIRECTORIES = [
+        "quorum"
+      ]
+
+      def copy_styles
+        STYLE_DIRECTORIES.each do |d|
+          directory d.to_s, "app/assets/stylesheets/#{d.to_s}"
+        end
+      end
+    end
+  end
+end

data/lib/generators/quorum/views_generator.rb

@@ -0,0 +1,18 @@
+module Quorum
+  module Generators
+    class ViewsGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../../../app/views/quorum", __FILE__)
+      desc "Copy quorum views to your application."
+
+      VIEW_DIRECTORIES = [
+        "jobs"
+      ]
+
+      def copy_views
+        VIEW_DIRECTORIES.each do |d|
+          directory d.to_s, "app/views/quorum/#{d.to_s}"
+        end
+      end
+    end
+  end
+end

data/lib/generators/templates/README

@@ -0,0 +1,25 @@
+
+ZOMG!! Thanks for installing Quorum!!
+
+==============================================================================
+
+Quorum Manual Setup:
+
+1. Ensure you have defined root_url in your config/routes.rb.
+   If you are deploying Quorum as a standalone application, 
+   add the below after the engine is mounted. 
+
+     mount Quorum::Engine => "/quorum"
+
+     match "/" => redirect("/quorum")
+
+2. Build your Blast databases.
+
+     rake quorum:blastdb:build
+
+   For all available quorum:blastdb:build options
+
+     rake -D 
+
+==============================================================================
+