quorum 0.3.0 → 0.3.1

data/lib/quorum/sequence.rb

@@ -13,7 +13,7 @@ module Quorum
     # to ensure FASTA format.
     #
     def write_input_sequence_to_file(tmp_dir, hash, sequence)
-      seq = File.join(tmp_dir, hash + ".seq") 
+      seq = File.join(tmp_dir, hash + ".seq")
       File.open(seq, "w") do |f|
         f << sequence
       end
@@ -35,19 +35,19 @@ module Quorum
     #
     # Subtracting all AA single letter chars from NA single letter chars
     # (including ALL ambiguity codes for each!) leaves us with
-    # EQILFP. If a sequence contains EQILFP, it's safe to call it an AA. 
+    # EQILFP. If a sequence contains EQILFP, it's safe to call it an AA.
     #
     # See single letter char tables for more information:
     # http://en.wikipedia.org/wiki/Proteinogenic_amino_acid
     # http://www.chick.manchester.ac.uk/SiteSeer/IUPAC_codes.html
     #
-    # If a sequence doesn't contain EQILFP, it could be either an AA 
+    # If a sequence doesn't contain EQILFP, it could be either an AA
     # or NA. To distinguish the two, count the number of As Ts Gs Cs
     # and Ns, divide by the the length of the sequence and * 100.
     #
     # If the percentage of A, T, U, G, C or N is >= 15.0, call it a NA.
-    # 15% was choosen based on the data in the table 
-    # "Relative proportions (%) of bases in DNA" 
+    # 15% was choosen based on the data in the table
+    # "Relative proportions (%) of bases in DNA"
     # (http://en.wikipedia.org/wiki/Chargaff's_rules) and the
     # precentage of AAs found in peptides
     # (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2590925/).
@@ -75,7 +75,7 @@ module Quorum
 
         n = (seq.count("N").to_f / len) * 100
 
-        if (a >= na_percent) || (t >= na_percent) || (u >= na_percent) || 
+        if (a >= na_percent) || (t >= na_percent) || (u >= na_percent) ||
           (g >= na_percent) || (c >= na_percent) || (n >= na_percent)
           type = "nucleic_acid"
         else

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.3.0"
+  VERSION = "0.3.1"
 end

data/lib/quorum.rb

@@ -12,7 +12,7 @@ module Quorum
   ## Supported Algorithms ##
   BLAST_ALGORITHMS = ["blastn", "blastx", "blastp", "tblastn"]
 
-  mattr_accessor :blast_remote, :blast_ssh_host, :blast_ssh_user, 
+  mattr_accessor :blast_remote, :blast_ssh_host, :blast_ssh_user,
     :blast_ssh_options, :blast_bin, :blast_log_dir, :blast_tmp_dir,
     :blast_db, :tblastn, :blastp, :blastn, :blastx, :blast_threads
 

data/lib/tasks/blastdb/build_blast_db.rb

@@ -56,14 +56,14 @@ module Quorum
         Dir.mkdir(@log_dir) unless File.directory?(@log_dir)
       rescue SystemCallError => e
         @output.puts e.message
-        raise "Unable to make directory. " << 
+        raise "Unable to make directory. " <<
           "Perhaps you forgot to execute the quorum initializer. \n\n" <<
           "rails generate quorum:install"
       end
     end
 
     #
-    # Create directories per tarball and return tarball file name 
+    # Create directories per tarball and return tarball file name
     # minus the file extension.
     #
     def create_file_name(file, base_dir)
@@ -120,7 +120,7 @@ module Quorum
           contigs  = File.join(d, "contigs.fa")
           peptides = File.join(d, "peptides.fa")
 
-          found = false 
+          found = false
 
           if File.exists?(contigs) && File.readable?(contigs)
             execute_makeblastdb("nucl", d, contigs)
@@ -164,7 +164,7 @@ module Quorum
       end
 
       unless VALID_TYPES.include?(@type)
-        raise "Unknown type: #{@type}. " << 
+        raise "Unknown type: #{@type}. " <<
           "Please provide one: both, nucl or prot."
       end
 
@@ -174,7 +174,7 @@ module Quorum
 
       begin
         @dir.split(':').each do |d|
-          unless File.directory?(d)    
+          unless File.directory?(d)
             raise "Directory not found: #{d}"
           end
 
@@ -187,11 +187,11 @@ module Quorum
 
           @data.each do |s|
             if s =~ GZIP
-              files = `tar -tzf #{s}` 
+              files = `tar -tzf #{s}`
               flag  = "z"
             elsif s =~ BZIP
               files = `tar -tjf #{s}`
-              flag  = "j"       
+              flag  = "j"
             end
             files = files.split(/\n/)
             files.each do |f|

data/lib/tasks/quorum_tasks.rake

@@ -8,10 +8,10 @@ require 'build_blast_db'
 
 namespace :quorum do
   namespace :blastdb do
-    desc "Build Blast Database (options: DIR=/path/to/data " << 
-    "{valid extensions: .tar.gz .tgz .tar.bz2 .tbz} " << 
-    "-- separate multiple directories with a colon. " << 
-    "TYPE={both}{prot}{nucl} -- defaults to both. " << 
+    desc "Build Blast Database (options: DIR=/path/to/data " <<
+    "{valid extensions: .tar.gz .tgz .tar.bz2 .tbz} " <<
+    "-- separate multiple directories with a colon. " <<
+    "TYPE={both}{prot}{nucl} -- defaults to both. " <<
     "PROT_FILE_NAME= -- defaults to peptides.fa. " <<
     "NUCL_FILE_NAME= -- defaults to contigs.fa. " <<
     "REBUILD_DB= {true or false} -- remove existing blast database(s). " <<
@@ -39,9 +39,9 @@ namespace :quorum do
       args[:nucl_file] = args[:nucl_file].downcase.strip
       args[:nucl_file] = "NULL" if args[:type] == "prot"
       args[:prot_file] = "NULL" if args[:type] == "nucl"
-      
+
       puts "Building your Blast database(s). This may take a while..."
-      
+
       build = Quorum::BuildBlastDB.new(args)
       build.build_blast_db_data
     end

data/lib/workers/quorum.rb

@@ -1,4 +1,4 @@
-module Workers 
+module Workers
   class System
     extend Resque::Plugins::Result
 
@@ -24,7 +24,7 @@ module Workers
         Net::SSH.start(ssh_host, ssh_user, ssh_options) do |ssh|
           ssh.open_channel do |ch|
             ch.exec(cmd) do |ch, success|
-              unless success 
+              unless success
                 Rails.logger.warn "Channel Net::SSH exec() failed. :'("
               else
                 # Capture STDOUT from ch.exec()

data/quorum.gemspec

@@ -13,7 +13,7 @@ Gem::Specification.new do |s|
   s.summary     = "Flexible bioinformatics search tool."
   s.description = "Flexible bioinformatics search tool."
 
-  s.files = `git ls-files`.split(/\n/) 
+  s.files = `git ls-files`.split(/\n/)
 
   s.add_dependency "rails", "~> 3.1"
   s.add_dependency "jquery-rails"

data/spec/javascripts/fixtures/quorum_search_form.html

@@ -12,7 +12,7 @@
     <!-- blastn -->
 
     <p>
-    <strong>blastn</strong> 
+    <strong>blastn</strong>
     <input name="job[blastn_job_attributes][queue]" type="hidden" value="0" /><input id="job_blastn_job_attributes_queue" name="job[blastn_job_attributes][queue]" type="checkbox" value="1" />
     </p>
     <div id="blastn" class="toggle">
@@ -57,7 +57,7 @@
                         <option value="taxus_x_media-20100126">Taxus x media transcripts, build 20100126</option>
                         <option value="taxus_x_media-20100406">Taxus x media transcripts, build 20100406</option>
                         <option value="taxus_x_media-20101112">Taxus x media transcripts, build 20101112</option>
-                        <option value="medp_trire-20110120">Tripterygium regelii transcripts, build 20110120</option></select> 
+                        <option value="medp_trire-20110120">Tripterygium regelii transcripts, build 20110120</option></select>
                 </td>
                 <td>
                     <label for="job_blastn_job_attributes_filter">DUST</label>
@@ -124,7 +124,7 @@
     <!-- blastx -->
 
     <p>
-    <strong>blastx</strong> 
+    <strong>blastx</strong>
     <input name="job[blastx_job_attributes][queue]" type="hidden" value="0" /><input id="job_blastx_job_attributes_queue" name="job[blastx_job_attributes][queue]" type="checkbox" value="1" />
     </p>
     <div id="blastx" class="toggle">
@@ -167,7 +167,7 @@
                         <option value="podophyllum_peltatum-20101112">Podophyllum peltatum peptides, build 20101112</option>
                         <option value="taxus_x_media-20100406">Taxus x media peptides, build 20100406</option>
                         <option value="taxus_x_media-20101112">Taxus x media peptides, build 20101112</option>
-                        <option value="medp_trire-20110120">Tripterygium regelii peptides, build 20110120</option></select> 
+                        <option value="medp_trire-20110120">Tripterygium regelii peptides, build 20110120</option></select>
                 </td>
                 <td>
                     <label for="job_blastx_job_attributes_filter">SEG</label>
@@ -234,7 +234,7 @@
     <!-- tblastn -->
 
     <p>
-    <strong>tblastn</strong> 
+    <strong>tblastn</strong>
     <input name="job[tblastn_job_attributes][queue]" type="hidden" value="0" /><input id="job_tblastn_job_attributes_queue" name="job[tblastn_job_attributes][queue]" type="checkbox" value="1" />
     </p>
     <div id="tblastn" class="toggle">
@@ -279,7 +279,7 @@
                         <option value="taxus_x_media-20100126">Taxus x media transcripts, build 20100126</option>
                         <option value="taxus_x_media-20100406">Taxus x media transcripts, build 20100406</option>
                         <option value="taxus_x_media-20101112">Taxus x media transcripts, build 20101112</option>
-                        <option value="medp_trire-20110120">Tripterygium regelii transcripts, build 20110120</option></select> 
+                        <option value="medp_trire-20110120">Tripterygium regelii transcripts, build 20110120</option></select>
                 </td>
                 <td>
                     <label for="job_tblastn_job_attributes_filter">SEG</label>
@@ -346,7 +346,7 @@
     <!-- blastp -->
 
     <p>
-    <strong>blastp</strong> 
+    <strong>blastp</strong>
     <input name="job[blastp_job_attributes][queue]" type="hidden" value="0" /><input id="job_blastp_job_attributes_queue" name="job[blastp_job_attributes][queue]" type="checkbox" value="1" />
     </p>
     <div id="blastp" class="toggle">
@@ -389,7 +389,7 @@
                         <option value="podophyllum_peltatum-20101112">Podophyllum peltatum peptides, build 20101112</option>
                         <option value="taxus_x_media-20100406">Taxus x media peptides, build 20100406</option>
                         <option value="taxus_x_media-20101112">Taxus x media peptides, build 20101112</option>
-                        <option value="medp_trire-20110120">Tripterygium regelii peptides, build 20110120</option></select> 
+                        <option value="medp_trire-20110120">Tripterygium regelii peptides, build 20110120</option></select>
                 </td>
                 <td>
                     <label for="job_blastp_job_attributes_filter">SEG</label>

data/spec/javascripts/quorum_spec.js

@@ -4,50 +4,50 @@
 
 describe("QUORUM", function() {
 
-  // 
+  //
   // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
   //
   // Blastn should increment qseq's title by 1 and hseq's title by 1.
   //
   it("formats blastn sequence report for Blast detailed report", function() {
     var report = QUORUM.formatSequenceReport(
-      "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastn"  
+      "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastn"
     );
     expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=7>C</a><a rel='quorum-tipsy' title=8>G</a><a rel='quorum-tipsy' title=9>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
   });
 
-  // 
+  //
   // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
   //
   // Blastx should increment qseq's title by 3 and hseq's title by 1.
   //
   it("formats blastx sequence report for Blast detailed report", function() {
     var report = QUORUM.formatSequenceReport(
-      "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastx"  
+      "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastx"
     );
     expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=9>C</a><a rel='quorum-tipsy' title=12>G</a><a rel='quorum-tipsy' title=15>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
   });
 
-  // 
+  //
   // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
   //
   // Tblastn should increment qseq's title by 1 and hseq's title by 3.
   //
   it("formats tblastn sequence report for Blast detailed report", function() {
     var report = QUORUM.formatSequenceReport(
-      "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 136, "tblastn"  
+      "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 136, "tblastn"
     );
     expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=124>L</a><a rel='quorum-tipsy' title=127>V</a><a rel='quorum-tipsy' title=130>I</a><a rel='quorum-tipsy' title=133>S</a>\n\n</pre></span>");
   });
 
-  // 
+  //
   // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
   //
   // Blastp should increment qseq's title by 1 and hseq's title by 1.
   //
   it("formats blastx sequence report for Blast detailed report", function() {
     var report = QUORUM.formatSequenceReport(
-      "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 125, "blastp"  
+      "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 125, "blastp"
     );
     expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=122>L</a><a rel='quorum-tipsy' title=123>V</a><a rel='quorum-tipsy' title=124>I</a><a rel='quorum-tipsy' title=125>S</a>\n\n</pre></span>");
   });
@@ -65,19 +65,19 @@ describe("QUORUM", function() {
 
   it("prints hit strand as forward / forward for + / + intergers", function() {
     expect(QUORUM.formatStrand(1, 1)).toEqual("forward / forward");
-  }); 
+  });
 
   it("prints hit strand as forward / reverse for + / - integers", function() {
     expect(QUORUM.formatStrand(1, -1)).toEqual("forward / reverse");
-  }); 
+  });
 
   it("prints hit strand as reverse / forward for - / + integers", function() {
     expect(QUORUM.formatStrand(-1, 1)).toEqual("reverse / forward");
-  }); 
+  });
 
   it("prints hit strand as reverse / reverse for - / - integers", function() {
     expect(QUORUM.formatStrand(-1, -1)).toEqual("reverse / reverse");
-  }); 
+  });
 
   //
   // Only print links to HSPs whers data id != focus.

data/spec/javascripts/string_spec.js

@@ -2,12 +2,12 @@ describe("String", function() {
 
   it("truncates a string to length n", function() {
     var str = "this is a long string.";
-    expect(str.trunc(5)).toEqual("this...");    
+    expect(str.trunc(5)).toEqual("this...");
   });
 
   it("truncates a string to length n", function() {
     var str = "this is a long string.";
-    expect(str.trunc(15)).toEqual("this is a long...");    
+    expect(str.trunc(15)).toEqual("this is a long...");
   });
 
   it("doesn't truncate string when length is less than n", function() {

data/spec/models/blastn_job_report_spec.rb

@@ -1,13 +1,13 @@
 require 'spec_helper'
 
 describe Quorum::BlastnJobReport do
-  
+
   it "should respond to default_order" do
-    Quorum::BlastnJobReport.methods.should include(:default_order) 
+    Quorum::BlastnJobReport.methods.should include(:default_order)
   end
 
   it "should respond to by_query" do
-    Quorum::BlastnJobReport.methods.should include(:by_query) 
+    Quorum::BlastnJobReport.methods.should include(:by_query)
   end
 
 end

data/spec/models/blastp_job_report_spec.rb

@@ -1,13 +1,13 @@
 require 'spec_helper'
 
 describe Quorum::BlastpJobReport do
-  
+
   it "should respond to default_order" do
-    Quorum::BlastpJobReport.methods.should include(:default_order) 
+    Quorum::BlastpJobReport.methods.should include(:default_order)
   end
 
   it "should respond to by_query" do
-    Quorum::BlastpJobReport.methods.should include(:by_query) 
+    Quorum::BlastpJobReport.methods.should include(:by_query)
   end
 
 end

data/spec/models/blastx_job_report_spec.rb

@@ -1,13 +1,13 @@
 require 'spec_helper'
 
 describe Quorum::BlastxJobReport do
-  
+
   it "should respond to default_order" do
-    Quorum::BlastxJobReport.methods.should include(:default_order) 
+    Quorum::BlastxJobReport.methods.should include(:default_order)
   end
 
   it "should respond to default_order" do
-    Quorum::BlastxJobReport.methods.should include(:by_query) 
+    Quorum::BlastxJobReport.methods.should include(:by_query)
   end
 
 end

data/spec/models/job_spec.rb

@@ -1,7 +1,7 @@
 require 'spec_helper'
 
 describe Quorum::Job do
-  
+
   before(:each) do
     @job = Quorum::Job.new()
     ResqueSpec.reset!

data/spec/models/tblastn_job_report_spec.rb

@@ -1,13 +1,13 @@
 require 'spec_helper'
 
 describe Quorum::TblastnJobReport do
-  
+
   it "should respond to default_order" do
-    Quorum::TblastnJobReport.methods.should include(:default_order) 
+    Quorum::TblastnJobReport.methods.should include(:default_order)
   end
 
   it "should respond to default_order" do
-    Quorum::TblastnJobReport.methods.should include(:by_query) 
+    Quorum::TblastnJobReport.methods.should include(:by_query)
   end
 
 end

data/spec/quorum/quorum_sequence_spec.rb

@@ -9,7 +9,7 @@ describe "Quorum::Sequence" do
       sequence = File.open(
         File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
       ).read
-      create_hash(sequence).should_not be_nil 
+      create_hash(sequence).should_not be_nil
     end
   end
 

data/spec/requests/jobs_spec.rb

@@ -16,7 +16,7 @@ describe "Jobs" do
       fill_in "job_sequence", :with => ""
       click_button "Submit"
 
-      page.should have_content("Please enter your sequence(s) in Plain Text " << 
+      page.should have_content("Please enter your sequence(s) in Plain Text " <<
                                "as FASTA.")
     end
   end
@@ -29,7 +29,7 @@ describe "Jobs" do
       word_file = File.expand_path("../../data/seqs.docx", __FILE__)
       attach_file "job_sequence_file", word_file
       click_button "Submit"
-      page.should have_content("Please enter your sequence(s) in Plain Text " << 
+      page.should have_content("Please enter your sequence(s) in Plain Text " <<
                                "as FASTA.")
     end
   end
@@ -42,14 +42,15 @@ describe "Jobs" do
       file = File.expand_path("../../data/seqs_not_fa.txt", __FILE__)
       attach_file "job_sequence_file", file
       click_button "Submit"
-      page.should have_content("Please enter your sequence(s) in Plain Text " << 
+      page.should have_content("Please enter your sequence(s) in Plain Text " <<
                                "as FASTA.")
     end
   end
 
   context "javascript", @javascript do
     before(:all) do
-      Capybara.current_driver = :selenium
+      Capybara.current_driver    = :selenium
+      Capybara.default_wait_time = 5
     end
     before(:each) do
       ResqueSpec.reset!
@@ -65,7 +66,7 @@ describe "Jobs" do
 
         # Blastn
         check "job_blastn_job_attributes_queue"
-        select "tmp", :from => "job_blastn_job_attributes_blast_dbs" 
+        select "tmp", :from => "job_blastn_job_attributes_blast_dbs"
         check "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"
@@ -75,7 +76,7 @@ describe "Jobs" do
 
         # Blastx
         check "job_blastx_job_attributes_queue"
-        select "tmp", :from => "job_blastx_job_attributes_blast_dbs" 
+        select "tmp", :from => "job_blastx_job_attributes_blast_dbs"
         check "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"
@@ -85,7 +86,7 @@ describe "Jobs" do
 
         # Tblastn
         check "job_tblastn_job_attributes_queue"
-        select "tmp", :from => "job_tblastn_job_attributes_blast_dbs" 
+        select "tmp", :from => "job_tblastn_job_attributes_blast_dbs"
         check "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"
@@ -95,7 +96,7 @@ describe "Jobs" do
 
         # Blastp
         check "job_blastp_job_attributes_queue"
-        select "tmp", :from => "job_blastp_job_attributes_blast_dbs" 
+        select "tmp", :from => "job_blastp_job_attributes_blast_dbs"
         check "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"
@@ -105,13 +106,13 @@ describe "Jobs" do
 
         click_button "Submit"
 
-        page.should have_content("Search Results") 
+        page.should have_content("Search Results")
 
         click_link "Blastx"
-        page.should have_content("Your search returned 0 hits.") 
+        page.should have_content("Your search returned 0 hits.")
 
         click_link "Tblastn"
-        page.should have_content("Your search returned 0 hits.") 
+        page.should have_content("Your search returned 0 hits.")
 
         ## Interact with the Blast results. ##
         click_link "Blastn"

data/spec/spec_helper.rb

@@ -72,5 +72,5 @@ RSpec.configure do |config|
       cat #{REDIS_PID} | xargs kill -QUIT
       rm -f #{REDIS_CACHE_PATH}dump.rdb
     }
-  end 
+  end
 end

data/spec/tasks/blastdb_rake_spec.rb

@@ -23,12 +23,12 @@ describe "blastdb rake tasks" do
         )
       }
     end
-    
+
     it "raises exception without DIR argument" do
       expect {
         Quorum::BuildBlastDB.new({}).build_blast_db_data
       }.to raise_error(
-        RuntimeError, 
+        RuntimeError,
         'DIR must be set to continue. Execute `rake -D` for more information.'
       )
     end
@@ -38,7 +38,7 @@ describe "blastdb rake tasks" do
       expect {
         Quorum::BuildBlastDB.new(@args).build_blast_db_data
       }.to raise_error(
-        RuntimeError, 
+        RuntimeError,
         "Unknown type: #{@args[:type]}. Please provide one: both, nucl or prot."
       )
     end
@@ -80,7 +80,7 @@ describe "blastdb rake tasks" do
       @build = Quorum::BuildBlastDB.new(@args, output)
 
       expect {
-        @build.build_blast_db_data 
+        @build.build_blast_db_data
       }.to_not raise_error
 
       File.directory?(@args[:blastdb_dir]).should be_true
@@ -95,7 +95,7 @@ describe "blastdb rake tasks" do
 
       @args[:empty] = false
       @build = Quorum::BuildBlastDB.new(@args, output)
-      
+
       expect {
         @build.build_blast_db_data
       }.to_not raise_error

data/spec/templates/blast_spec.rb

@@ -42,7 +42,7 @@ describe "Quorum::SearchTools::Blast" do
       @job.blastp_job.queue     = true
       @job.blastp_job.blast_dbs = ["test"]
     end
-  
+
     it "executes blastn on a given dataset" do
       @job.stub(:queue_workers)
       @job.save!
@@ -57,7 +57,7 @@ describe "Quorum::SearchTools::Blast" do
       Dir.glob(
         File.join(@args[:tmp_directory], "*")
       ).length.should be == 0
-    end 
+    end
 
     it "executes blastx on a given dataset" do
       @job.stub(:queue_workers)
@@ -74,7 +74,7 @@ describe "Quorum::SearchTools::Blast" do
       Dir.glob(
         File.join(@args[:tmp_directory], "*")
       ).length.should be == 0
-    end 
+    end
 
     it "executes tblastn on a given dataset" do
       @job.stub(:queue_workers)
@@ -91,7 +91,7 @@ describe "Quorum::SearchTools::Blast" do
       Dir.glob(
         File.join(@args[:tmp_directory], "*")
       ).length.should be == 0
-    end 
+    end
 
     it "executes blastp on a given dataset" do
       @job.stub(:queue_workers)
@@ -108,7 +108,7 @@ describe "Quorum::SearchTools::Blast" do
       Dir.glob(
         File.join(@args[:tmp_directory], "*")
       ).length.should be == 0
-    end 
+    end
 
   end
 end