quorum 0.5.2 → 0.6.0

data/spec/models/blastx_job_spec.rb

@@ -6,12 +6,12 @@ describe Quorum::BlastxJob do
     @blastx_job = Quorum::BlastxJob.new()
   end
 
-  it "fails validation with poorly formatted expectation (using error_on)" do
+  it "fails validation with poorly formatted expectation" do
     @blastx_job.expectation = "this is bad"
     @blastx_job.should have(1).error_on(:expectation)
   end
 
-  it "passes validation with valid expectation values (using error_on)" do
+  it "passes validation with valid expectation values" do
     @blastx_job.expectation = 12
     @blastx_job.should have(0).errors_on(:expectation)
     @blastx_job.expectation = 12.1201
@@ -22,49 +22,49 @@ describe Quorum::BlastxJob do
     @blastx_job.should have(0).errors_on(:expectation)
   end
 
-  it "fails validation with poorly formatted max_score (using error_on)" do
-    @blastx_job.max_score = 12.34
-    @blastx_job.should have(1).error_on(:max_score)
-    @blastx_job.max_score = "not a number"
-    @blastx_job.should have(1).error_on(:max_score)
+  it "fails validation with poorly formatted max_target_seqs" do
+    @blastx_job.max_target_seqs = 12.34
+    @blastx_job.should have(1).error_on(:max_target_seqs)
+    @blastx_job.max_target_seqs = "not a number"
+    @blastx_job.should have(1).error_on(:max_target_seqs)
   end
 
-  it "passed validation with valid max_score (using error_on)" do
-    @blastx_job.max_score = 1235
-    @blastx_job.should have(0).errors_on(:max_score)
+  it "passed validation with valid max_target_seqs" do
+    @blastx_job.max_target_seqs = 1235
+    @blastx_job.should have(0).errors_on(:max_target_seqs)
   end
 
-  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_opening_penalty" do
     @blastx_job.gap_opening_penalty = "not a number"
     @blastx_job.should have(1).error_on(:gap_opening_penalty)
     @blastx_job.gap_opening_penalty = 100.10
     @blastx_job.should have(1).error_on(:gap_opening_penalty)
   end
 
-  it "passed validation with valid gap_opening_penalty (using error_on)" do
-    @blastx_job.max_score = 13
+  it "passed validation with valid gap_opening_penalty" do
+    @blastx_job.max_target_seqs = 13
     @blastx_job.should have(0).errors_on(:gap_opening_penalty)
   end
 
-  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_extension_penalty" do
     @blastx_job.gap_extension_penalty = "who are you?"
     @blastx_job.should have(1).error_on(:gap_extension_penalty)
     @blastx_job.gap_extension_penalty = 0.3
     @blastx_job.should have(1).error_on(:gap_extension_penalty)
   end
 
-  it "passed validation with valid gap_extension_penalty (using error_on)" do
-    @blastx_job.max_score = 456
+  it "passed validation with valid gap_extension_penalty" do
+    @blastx_job.max_target_seqs = 456
     @blastx_job.should have(0).errors_on(:gap_extension_penalty)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "passes validation without selecting gap_opening_extension with gapped_alignment" do
     @blastx_job.gapped_alignments = true
     @blastx_job.gap_opening_extension = ""
-    @blastx_job.should have(1).error_on(:gap_opening_extension)
+    @blastx_job.should have(0).error_on(:gap_opening_extension)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "fails validation without selecting gap_opening_extension with gapped_alignment" do
     @blastx_job.gapped_alignments = true
     @blastx_job.gap_opening_extension = "11, 2"
     @blastx_job.should have(0).errors_on(:gap_opening_extension)
@@ -100,6 +100,25 @@ describe Quorum::BlastxJob do
     )
   end
 
+  it "passes validation if not enqueued and blast_dbs is empty" do
+    @blastx_job.queue = false
+    @blastx_job.blast_dbs = []
+    @blastx_job.should have(0).errors_on(:blast_dbs)
+  end
+
+  it "fails validation if blast_dbs is empty" do
+    @blastx_job.queue = true
+    @blastx_job.blast_dbs = []
+    @blastx_job.should have(1).errors_on(:blast_dbs)
+  end
+
+  # Test for removal of multiple select hidden field value.
+  it "fails validation if blast_dbs contains an empty string" do
+    @blastx_job.queue = true
+    @blastx_job.blast_dbs = ["", "", ""]
+    @blastx_job.should have(1).errors_on(:blast_dbs)
+  end
+
   it "joins blast_dbs on semicolon after save" do
     @blastx_job.blast_dbs = ["test_1", "test_2"]
     @blastx_job.save
@@ -109,10 +128,10 @@ describe Quorum::BlastxJob do
   it "sets optional params to default values if empty after save" do
     @blastx_job.save
     @blastx_job.expectation.should eq("5e-20")
-    @blastx_job.max_score.should eq(25)
+    @blastx_job.max_target_seqs.should eq(25)
     @blastx_job.min_bit_score.should eq(0)
-    @blastx_job.gap_opening_penalty.should eq(0)
-    @blastx_job.gap_extension_penalty.should eq(0)
+    @blastx_job.gap_opening_penalty.should be_nil
+    @blastx_job.gap_extension_penalty.should be_nil
   end
 
 end

data/spec/models/job_spec.rb

@@ -7,7 +7,7 @@ describe Quorum::Job do
     ResqueSpec.reset!
   end
 
-  it "fails validation without params (using error_on)" do
+  it "fails validation without params" do
     @job.should have(1).error_on(:sequence)
     @job.should have(1).error_on(:algorithm)
   end

data/spec/models/tblastn_job_spec.rb

@@ -6,12 +6,12 @@ describe Quorum::TblastnJob do
     @tblastn_job = Quorum::TblastnJob.new()
   end
 
-  it "fails validation with poorly formatted expectation (using error_on)" do
+  it "fails validation with poorly formatted expectation" do
     @tblastn_job.expectation = "this is bad"
     @tblastn_job.should have(1).error_on(:expectation)
   end
 
-  it "passes validation with valid expectation values (using error_on)" do
+  it "passes validation with valid expectation values" do
     @tblastn_job.expectation = 12
     @tblastn_job.should have(0).errors_on(:expectation)
     @tblastn_job.expectation = 12.1201
@@ -22,49 +22,49 @@ describe Quorum::TblastnJob do
     @tblastn_job.should have(0).errors_on(:expectation)
   end
 
-  it "fails validation with poorly formatted max_score (using error_on)" do
-    @tblastn_job.max_score = 12.34
-    @tblastn_job.should have(1).error_on(:max_score)
-    @tblastn_job.max_score = "not a number"
-    @tblastn_job.should have(1).error_on(:max_score)
+  it "fails validation with poorly formatted max_target_seqs" do
+    @tblastn_job.max_target_seqs = 12.34
+    @tblastn_job.should have(1).error_on(:max_target_seqs)
+    @tblastn_job.max_target_seqs = "not a number"
+    @tblastn_job.should have(1).error_on(:max_target_seqs)
   end
 
-  it "passed validation with valid max_score (using error_on)" do
-    @tblastn_job.max_score = 1235
-    @tblastn_job.should have(0).errors_on(:max_score)
+  it "passed validation with valid max_target_seqs" do
+    @tblastn_job.max_target_seqs = 1235
+    @tblastn_job.should have(0).errors_on(:max_target_seqs)
   end
 
-  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_opening_penalty" do
     @tblastn_job.gap_opening_penalty = "not a number"
     @tblastn_job.should have(1).error_on(:gap_opening_penalty)
     @tblastn_job.gap_opening_penalty = 100.10
     @tblastn_job.should have(1).error_on(:gap_opening_penalty)
   end
 
-  it "passed validation with valid gap_opening_penalty (using error_on)" do
-    @tblastn_job.max_score = 13
+  it "passed validation with valid gap_opening_penalty" do
+    @tblastn_job.max_target_seqs = 13
     @tblastn_job.should have(0).errors_on(:gap_opening_penalty)
   end
 
-  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_extension_penalty" do
     @tblastn_job.gap_extension_penalty = "who are you?"
     @tblastn_job.should have(1).error_on(:gap_extension_penalty)
     @tblastn_job.gap_extension_penalty = 0.3
     @tblastn_job.should have(1).error_on(:gap_extension_penalty)
   end
 
-  it "passed validation with valid gap_extension_penalty (using error_on)" do
-    @tblastn_job.max_score = 456
+  it "passed validation with valid gap_extension_penalty" do
+    @tblastn_job.max_target_seqs = 456
     @tblastn_job.should have(0).errors_on(:gap_extension_penalty)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "passes validation without selecting gap_opening_extension with gapped_alignment" do
     @tblastn_job.gapped_alignments = true
     @tblastn_job.gap_opening_extension = ""
-    @tblastn_job.should have(1).error_on(:gap_opening_extension)
+    @tblastn_job.should have(0).error_on(:gap_opening_extension)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "fails validation without selecting gap_opening_extension with gapped_alignment" do
     @tblastn_job.gapped_alignments = true
     @tblastn_job.gap_opening_extension = "11, 2"
     @tblastn_job.should have(0).errors_on(:gap_opening_extension)
@@ -100,6 +100,25 @@ describe Quorum::TblastnJob do
     )
   end
 
+  it "passes validation if not enqueued and blast_dbs is empty" do
+    @tblastn_job.queue = false
+    @tblastn_job.blast_dbs = []
+    @tblastn_job.should have(0).errors_on(:blast_dbs)
+  end
+
+  it "fails validation if blast_dbs is empty" do
+    @tblastn_job.queue = true
+    @tblastn_job.blast_dbs = []
+    @tblastn_job.should have(1).errors_on(:blast_dbs)
+  end
+
+  # Test for removal of multiple select hidden field value.
+  it "fails validation if blast_dbs contains an empty string" do
+    @tblastn_job.queue = true
+    @tblastn_job.blast_dbs = ["", "", ""]
+    @tblastn_job.should have(1).errors_on(:blast_dbs)
+  end
+
   it "joins blast_dbs on semicolon after save" do
     @tblastn_job.blast_dbs = ["test_1", "test_2"]
     @tblastn_job.save
@@ -109,10 +128,10 @@ describe Quorum::TblastnJob do
   it "sets optional params to default values if empty after save" do
     @tblastn_job.save
     @tblastn_job.expectation.should eq("5e-20")
-    @tblastn_job.max_score.should eq(25)
+    @tblastn_job.max_target_seqs.should eq(25)
     @tblastn_job.min_bit_score.should eq(0)
-    @tblastn_job.gap_opening_penalty.should eq(0)
-    @tblastn_job.gap_extension_penalty.should eq(0)
+    @tblastn_job.gap_opening_penalty.should be_nil
+    @tblastn_job.gap_extension_penalty.should be_nil
   end
 
 end

data/spec/requests/jobs_spec.rb

@@ -68,40 +68,40 @@ describe "Jobs" do
         # Blastn
         check "job_blastn_job_attributes_queue"
         select "tmp", :from => "job_blastn_job_attributes_blast_dbs"
-        check "job_blastn_job_attributes_filter"
+        select "Yes", :from => "job_blastn_job_attributes_filter"
         fill_in "job_blastn_job_attributes_expectation", :with => "5e-20"
         fill_in "job_blastn_job_attributes_min_bit_score", :with => "0"
-        fill_in "job_blastn_job_attributes_max_score", :with => "25"
+        fill_in "job_blastn_job_attributes_max_target_seqs", :with => "25"
         select "Yes", :from => "job_blastn_job_attributes_gapped_alignments"
         select "11, 2", :from => "job_blastn_job_attributes_gap_opening_extension"
 
         # Blastx
         check "job_blastx_job_attributes_queue"
         select "tmp", :from => "job_blastx_job_attributes_blast_dbs"
-        check "job_blastx_job_attributes_filter"
+        select "Yes", :from => "job_blastx_job_attributes_filter"
         fill_in "job_blastx_job_attributes_expectation", :with => "5e-20"
         fill_in "job_blastx_job_attributes_min_bit_score", :with => "0"
-        fill_in "job_blastx_job_attributes_max_score", :with => "25"
+        fill_in "job_blastx_job_attributes_max_target_seqs", :with => "25"
         select "Yes", :from => "job_blastx_job_attributes_gapped_alignments"
         select "10, 2", :from => "job_blastx_job_attributes_gap_opening_extension"
 
         # Tblastn
         check "job_tblastn_job_attributes_queue"
         select "tmp", :from => "job_tblastn_job_attributes_blast_dbs"
-        check "job_tblastn_job_attributes_filter"
+        select "Yes", :from => "job_tblastn_job_attributes_filter"
         fill_in "job_tblastn_job_attributes_expectation", :with => "5e-20"
         fill_in "job_tblastn_job_attributes_min_bit_score", :with => "0"
-        fill_in "job_tblastn_job_attributes_max_score", :with => "25"
+        fill_in "job_tblastn_job_attributes_max_target_seqs", :with => "25"
         select "Yes", :from => "job_tblastn_job_attributes_gapped_alignments"
         select "9, 2", :from => "job_tblastn_job_attributes_gap_opening_extension"
 
         # Blastp
         check "job_blastp_job_attributes_queue"
         select "tmp", :from => "job_blastp_job_attributes_blast_dbs"
-        check "job_blastp_job_attributes_filter"
+        select "No", :from => "job_blastp_job_attributes_filter"
         fill_in "job_blastp_job_attributes_expectation", :with => "5e-20"
         fill_in "job_blastp_job_attributes_min_bit_score", :with => "0"
-        fill_in "job_blastp_job_attributes_max_score", :with => "25"
+        fill_in "job_blastp_job_attributes_max_target_seqs", :with => "25"
         select "Yes", :from => "job_blastp_job_attributes_gapped_alignments"
         select "13, 1", :from => "job_blastp_job_attributes_gap_opening_extension"
 

data/spec/templates/blast_db_spec.rb

@@ -1,5 +1,5 @@
 require 'spec_helper'
-require File.expand_path("../../dummy/quorum/lib/fetch_tools/blast_db", __FILE__)
+require 'generators/templates/blast_db'
 
 describe "Quorum::FetchTools::BlastDb" do
   describe "#execute_blast_db_cmd" do

data/spec/templates/blast_spec.rb

@@ -1,5 +1,5 @@
 require 'spec_helper'
-require File.expand_path("../../dummy/quorum/lib/search_tools/blast", __FILE__)
+require 'generators/templates/blast'
 
 describe "Quorum::SearchTools::Blast" do
   describe "#execute_blast non empty report" do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.5.2
+  version: 0.6.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-14 00:00:00.000000000 Z
+date: 2012-09-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -281,6 +281,7 @@ files:
 - db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb
 - db/migrate/20120807202555_add_gaps_to_blast_reports.rb
 - db/migrate/20120910175911_change_hsp_group_column_type.rb
+- db/migrate/20120918205556_rename_max_score_column.rb
 - lib/generators/quorum/images_generator.rb
 - lib/generators/quorum/install_generator.rb
 - lib/generators/quorum/styles_generator.rb
@@ -307,6 +308,7 @@ files:
 - lib/workers/quorum.rb
 - quorum.gemspec
 - script/rails
+- spec/config/quorum_settings.yml
 - spec/data/fake_seq.txt
 - spec/data/nucl_prot_seqs.txt
 - spec/data/nucl_seqs.txt
@@ -338,46 +340,18 @@ files:
 - spec/dummy/config/initializers/backtrace_silencers.rb
 - spec/dummy/config/initializers/inflections.rb
 - spec/dummy/config/initializers/mime_types.rb
-- spec/dummy/config/initializers/quorum_initializer.rb
 - spec/dummy/config/initializers/resque.rb
 - spec/dummy/config/initializers/secret_token.rb
 - spec/dummy/config/initializers/session_store.rb
 - spec/dummy/config/initializers/wrap_parameters.rb
 - spec/dummy/config/locales/en.yml
-- spec/dummy/config/locales/quorum.en.yml
-- spec/dummy/config/quorum_settings.yml
 - spec/dummy/config/routes.rb
-- spec/dummy/db/schema.rb
 - spec/dummy/lib/assets/.gitkeep
 - spec/dummy/log/.gitkeep
 - spec/dummy/public/404.html
 - spec/dummy/public/422.html
 - spec/dummy/public/500.html
 - spec/dummy/public/favicon.ico
-- spec/dummy/quorum/bin/fetch
-- spec/dummy/quorum/bin/search
-- spec/dummy/quorum/blastdb/test.nhd
-- spec/dummy/quorum/blastdb/test.nhi
-- spec/dummy/quorum/blastdb/test.nhr
-- spec/dummy/quorum/blastdb/test.nin
-- spec/dummy/quorum/blastdb/test.nog
-- spec/dummy/quorum/blastdb/test.nsd
-- spec/dummy/quorum/blastdb/test.nsi
-- spec/dummy/quorum/blastdb/test.nsq
-- spec/dummy/quorum/blastdb/test.phd
-- spec/dummy/quorum/blastdb/test.phi
-- spec/dummy/quorum/blastdb/test.phr
-- spec/dummy/quorum/blastdb/test.pin
-- spec/dummy/quorum/blastdb/test.pog
-- spec/dummy/quorum/blastdb/test.psd
-- spec/dummy/quorum/blastdb/test.psi
-- spec/dummy/quorum/blastdb/test.psq
-- spec/dummy/quorum/blastdb/test/contigs.fa
-- spec/dummy/quorum/blastdb/test/peptides.fa
-- spec/dummy/quorum/lib/fetch_tools/blast_db.rb
-- spec/dummy/quorum/lib/logger.rb
-- spec/dummy/quorum/lib/search_tools/blast.rb
-- spec/dummy/quorum/lib/trollop.rb
 - spec/dummy/script/rails
 - spec/javascripts/fixtures/formatted_sequence.html
 - spec/javascripts/fixtures/quorum_search_form.html
@@ -392,6 +366,7 @@ files:
 - spec/javascripts/support/jasmine.yml
 - spec/javascripts/support/jasmine_config.rb
 - spec/javascripts/support/jasmine_runner.rb
+- spec/lib/tasks/travis.rake
 - spec/models/blastn_job_report_spec.rb
 - spec/models/blastn_job_spec.rb
 - spec/models/blastp_job_report_spec.rb
@@ -427,7 +402,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 731925169058267446
+      hash: -238619027488195291
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -436,7 +411,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 731925169058267446
+      hash: -238619027488195291
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24

data/spec/dummy/config/initializers/quorum_initializer.rb

@@ -1,36 +0,0 @@
-## Quorum Settings ##
-#
-# DO NOT edit this file directly. To configure Quorum edit
-# config/quorum_settings.yml.
-
-## Load Quorum Setttings ##
-settings = YAML.load_file(
-  "#{::Rails.root.to_s}/config/quorum_settings.yml"
-)[::Rails.env.to_s]
-
-## Sub %{RAILS_ROOT} ##
-settings.keys.each do |k|
-  settings[k.to_s].each_value do |v|
-    if v.kind_of?(String)
-      v.to_s.gsub!('%{RAILS_ROOT}', ::Rails.root.to_s)
-    end
-  end
-end
-
-blast = settings['blast']
-
-## Quorum Blast Settings ##
-Quorum.blast_remote      = blast['remote']
-Quorum.blast_ssh_host    = blast['ssh_host']
-Quorum.blast_ssh_user    = blast['ssh_user']
-Quorum.blast_ssh_options = blast['ssh_options']
-Quorum.blast_bin         = blast['bin']
-Quorum.blast_log_dir     = blast['log_dir']
-Quorum.blast_tmp_dir     = blast['tmp_dir']
-Quorum.blast_db          = blast['blast_db']
-Quorum.tblastn           = blast['tblastn']
-Quorum.blastp            = blast['blastp']
-Quorum.blastn            = blast['blastn']
-Quorum.blastx            = blast['blastx']
-Quorum.blast_threads     = blast['blast_threads']
-

data/spec/dummy/config/locales/quorum.en.yml

@@ -1,8 +0,0 @@
-en:
-  quorum:
-    jobs:
-      errors:
-      notices:
-        data_not_found: "The data you requested is unavailable. Please check your URL and try again."
-      alerts:
-

data/spec/dummy/config/quorum_settings.yml

@@ -1,141 +0,0 @@
-# Quorum Settings
-#
-# ==> General
-# Quorum initializer safely substitutes %{RAILS_ROOT} with ::Rails.root.to_s.
-#
-# ==> NCBI BLAST+ Settings
-# blast:
-#   remote: true to execute script on remote machine via
-#     Net::SSH. false to execute locally via Kernel#system.
-#     See Net::SSH for more information.
-#     http://net-ssh.github.com/ssh/v2/api/index.html
-#
-#   ssh_host: Net::SSH.start() host.
-#
-#   ssh_user: Net::SSH.start() user.
-#
-#   ssh_options: Net::SSH.start() optional params.
-#     See http://net-ssh.github.com/ssh/v2/api/classes/Net/SSH.html#M000002
-#     for a complete list of options.
-#     Example Usage:
-#     ssh_options:
-#       password: "secret password"
-#       port: 8888
-#
-#   bin: Absolute path to quorum/bin.
-#
-#   log_dir: Absolute path to log file directory.
-#
-#   tmp_dir: Absolute path to tmp file directory.
-#
-#   blast_db: Absolute path to NCBI Blast database directory.
-#     Execute the rake task below to build your Blast DB.
-#     rake quorum:blastdb:build
-#
-#   blastn: Collection of Blast DBs under the parent blast_db
-#     to use with blastn.
-#     Example Usage:
-#     blastn:
-#       "Display name": blastn_database_name
-#       "A really cool genome": really_cool_genome
-#
-#   blastx: Collection of Blast DBs under the parent blast_db
-#     to use with blastx.
-#     Example Usage:
-#     blastx:
-#       "Display name": blastx_database_name
-#       "A really cool genome": really_cool_genome
-#
-#   tblastn: Collection of Blast DBs under the parent blast_db
-#     to use with tblastn.
-#     Example Usage:
-#     tblastn:
-#       "Display name": tblastn_database_name
-#       "A really cool genome": really_cool_genome
-#
-#   blastp: Collection of Blast DBs under the parent blast_db
-#     to use with blastp.
-#     Example Usage:
-#     blastp:
-#       "Display name": blastp_database_name
-#       "A really cool genome": really_cool_genome
-#
-#   blast_threads: Number of Blast threads. >= 1
-#     Defaults to 1.
-
-development:
-  blast:
-    remote: false
-    ssh_host:
-    ssh_user:
-    ssh_options:
-      # Example:
-      # password: "secret password"
-      # port: 8888
-    bin: "%{RAILS_ROOT}/quorum/bin"
-    log_dir: "%{RAILS_ROOT}/quorum/log"
-    tmp_dir: "%{RAILS_ROOT}/quorum/tmp"
-    blast_db: "%{RAILS_ROOT}/quorum/blastdb"
-    blastn:
-      "tmp": test
-    blastx:
-      "tmp": test
-    tblastn:
-      "tmp": test
-    blastp:
-      "tmp": test
-    blast_threads: 4
-
-test:
-  blast:
-    remote: false
-    ssh_host:
-    ssh_user:
-    ssh_options:
-      # Example:
-      # password: "secret password"
-      # port: 8888
-    bin: "%{RAILS_ROOT}/quorum/bin"
-    log_dir: "%{RAILS_ROOT}/quorum/log"
-    tmp_dir: "%{RAILS_ROOT}/quorum/tmp"
-    blast_db: "%{RAILS_ROOT}/quorum/blastdb"
-    blastn:
-      "tmp": test
-    blastx:
-      "tmp": test
-    tblastn:
-      "tmp": test
-    blastp:
-      "tmp": test
-    blast_threads:
-
-production:
-  blast:
-    remote: true
-    ssh_host:
-    ssh_user:
-    ssh_options:
-      # Example:
-      # password: "secret password"
-      # port: 8888
-    bin:
-    log_dir:
-    tmp_dir:
-    blast_db:
-    blastn:
-      # Example:
-      # "Display name": blastn_database_name
-      # "A really cool genome": really_cool_genome
-    blastx:
-      # Example:
-      # "Display name": blastx_database_name
-      # "A really cool genome": really_cool_genome
-    tblastn:
-      # Example:
-      # "Display name": tblastn_database_name
-      # "A really cool genome": really_cool_genome
-    blastp:
-      # Example:
-      # "Display name": blastp_database_name
-      # "A really cool genome": really_cool_genome
-    blast_threads: