genevalidator 1.6.12 → 2.1.3

data/Rakefile

@@ -1,16 +1,16 @@
 require 'rake/testtask'
+GEMSPEC = Gem::Specification.load('genevalidator.gemspec')
 
 task default: [:build]
 
 desc 'Builds and installs'
 task install: [:build] do
-  require_relative 'lib/genevalidator/version'
-  sh "gem install ./genevalidator-#{GeneValidator::VERSION}.gem"
+  sh "gem install #{Rake.original_dir}/genevalidator-#{GEMSPEC.version}.gem"
 end
 
 desc 'Runs tests, generates documentation, builds gem (default)'
-task build: [:test, :doc] do
-  sh 'gem build genevalidator.gemspec'
+task build: %i[test doc] do
+  sh "gem build #{Rake.original_dir}/genevalidator.gemspec"
 end
 
 desc 'Runs tests'
@@ -18,11 +18,383 @@ task :test do
   Rake::TestTask.new do |t|
     t.libs.push 'lib'
     t.test_files = FileList['test/test_*.rb']
-    t.verbose = true
+    t.verbose = false
+    t.warning = false
   end
 end
 
+desc 'Build Assets'
+task :assets do
+  # Requires uglifycss and uglifyjs
+  # npm install uglifycss -g
+  # npm install uglify-js -g
+  assets_dir = File.expand_path('aux/html_files', __dir__)
+  `rm #{assets_dir}/css/gv.compiled.min.css`
+  `rm #{assets_dir}/js/gv.compiled.min.js`
+  sh "uglifycss --output '#{assets_dir}/css/gv.compiled.min.css'" \
+     " '#{assets_dir}/css/src/font-awesome.min.css'" \
+     " '#{assets_dir}/css/src/bootstrap.min.css'" \
+     " '#{assets_dir}/css/src/style.css'"
+
+  sh "uglifyjs '#{assets_dir}/js/src/jquery-2.1.1.min.js'" \
+     " '#{assets_dir}/js/src/bootstrap.min.js'" \
+     " '#{assets_dir}/js/src/jquery.tablesorter.min.js'" \
+     " '#{assets_dir}/js/src/d3.v3.min.js'" \
+     " '#{assets_dir}/js/src/plots.js' '#{assets_dir}/js/src/script.js'" \
+     " -m -c -o '#{assets_dir}/js/gv.compiled.min.js'"
+end
+
 desc 'Generates documentation'
 task :doc do
   sh "yardoc 'lib/**/*.rb'"
 end
+
+##
+#### TRAVELLING RUBY
+##
+
+# For Bundler.with_clean_env
+require 'bundler/setup'
+
+TMP_DIR = "#{Rake.original_dir}/tmp".freeze
+APP_NAME = "#{GEMSPEC.name}-#{GEMSPEC.version}".freeze
+PLATFORMS = %w[linux-x86 linux-x86_64 osx].freeze
+TRAVELING_RUBY_VERSION = 'traveling-ruby-20150715-2.2.2'.freeze
+TRAVELING_RUBYGEMS_VERSION = 'traveling-ruby-gems-20150715-2.2.2'.freeze
+NOKOGIRI_VERSION = 'nokogiri-1.6.6.2'.freeze
+MAFFT = {
+  version: '7.397',
+  'linux-x86': 'https://mafft.cbrc.jp/alignment/software/mafft-7.397-linux.tgz',
+  'linux-x86_64': 'https://mafft.cbrc.jp/alignment/software/mafft-7.397-linux.tgz',
+  osx: 'https://mafft.cbrc.jp/alignment/software/mafft-7.397-mac.zip'
+}.freeze
+BLAST = {
+  version: '2.7.1+',
+  'linux-x86': 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz',
+  'linux-x86_64': 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz',
+  osx: 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-macosx.tar.gz'
+}.freeze
+JQ = {
+  version: '1.5',
+  'linux-x86': 'https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux32',
+  'linux-x86_64': 'https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64',
+  osx: 'https://github.com/stedolan/jq/releases/download/jq-1.5/jq-osx-amd64'
+}.freeze
+CSVTK = {
+  version: '0.14.0',
+  'linux-x86': 'https://github.com/shenwei356/csvtk/releases/download/v0.14.0/csvtk_linux_386.tar.gz',
+  'linux-x86_64': 'https://github.com/shenwei356/csvtk/releases/download/v0.14.0/csvtk_linux_amd64.tar.gz',
+  osx: 'https://github.com/shenwei356/csvtk/releases/download/v0.14.0/csvtk_darwin_amd64.tar.gz'
+}.freeze
+
+desc 'Create standalone GeneValidator packages'
+task :package do
+  rm_rf TMP_DIR
+  mkdir TMP_DIR
+  task('package:build' => ['package:linux-x86', 'package:linux-x86_64', 'package:osx']).invoke
+  rm_rf TMP_DIR
+end
+
+# Usage:
+# - Complete run
+#     rake package
+# - Just create directories and don't compress
+#     rake package DIR_ONLY=1
+namespace :package do
+  PLATFORMS.each do |platform|
+    task platform => [
+      :bundle_install, :reduce_bundle_size,
+      "#{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz",
+      "#{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}-#{NOKOGIRI_VERSION}.tar.gz"
+    ] do
+      package_dir   = "#{Rake.original_dir}/#{APP_NAME}-#{platform}"
+      lib_dir       = "#{package_dir}/lib/"
+      bin_dir       = "#{package_dir}/bin/"
+      exemplar_dir  = "#{package_dir}/exemplar_data/"
+      blast_db_dir  = "#{package_dir}/blast_db"
+      app_dir       = "#{lib_dir}/app/"
+      vendor_dir    = "#{lib_dir}/vendor/"
+      ruby_dir      = "#{lib_dir}/ruby/"
+      pack_dir      = "#{lib_dir}/packages/"
+      nokogiri_path = "#{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}-" \
+                      "#{NOKOGIRI_VERSION}.tar.gz"
+      ruby_path     = "#{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz"
+
+      # set up dir structure
+      rm_rf package_dir
+      mkdir_p app_dir
+      mkdir bin_dir
+      mkdir exemplar_dir
+      mkdir vendor_dir
+      mkdir ruby_dir
+      mkdir pack_dir
+
+      cp_r "#{Rake.original_dir}/bin", app_dir
+      cp_r "#{TMP_DIR}/vendor", lib_dir
+
+      cp "#{Rake.original_dir}/exemplar_data/mrna_data.fa", exemplar_dir
+      cp "#{Rake.original_dir}/exemplar_data/protein_data.fa", exemplar_dir
+
+      cd vendor_dir do
+        File.write('Gemfile', GEMFILE_CONTENTS)
+        mkdir '.bundle'
+        File.write('.bundle/config', BUNDLER_CONFIG)
+
+        sh "tar -xzf #{nokogiri_path} -C ruby"
+      end
+
+      cd lib_dir do
+        sh "tar -xzf #{ruby_path} -C ruby"
+      end
+
+      cd pack_dir do
+        process_package(MAFFT[platform.to_sym], 'mafft')
+        process_package(BLAST[platform.to_sym], 'blast')
+      end
+
+      cd package_dir do
+        File.write(GEMSPEC.name, SCRIPT_CONTENTS)
+        sh "chmod +x #{GEMSPEC.name}"
+        File.write('Readme.txt', readme_contents(platform))
+      end
+
+      cd bin_dir do
+        Dir['../lib/packages/blast/bin/*'].each do |bin|
+          ln_s bin, File.basename(bin)
+        end
+
+        # Copy a version of GV script into the bin directory
+        sh "sed 's|SELFDIR}/|SELFDIR}/../|g' #{package_dir}/#{GEMSPEC.name} > #{GEMSPEC.name}"
+        sh "chmod +x #{GEMSPEC.name}"
+
+        # Install JQ
+        sh "curl -L #{JQ[platform.to_sym]} -o jq"
+        sh 'chmod +x jq'
+
+        # Install CSVTK
+        sh "curl -L #{CSVTK[platform.to_sym]} | tar zxf -"
+      end
+
+      cp_r "#{TMP_DIR}/blast_db", blast_db_dir
+
+      unless ENV['DIR_ONLY']
+        cd Rake.original_dir do
+          sh "tar -czf #{APP_NAME}-#{platform}.tar.gz #{APP_NAME}-#{platform}"
+          rm_rf package_dir
+        end
+      end
+    end
+  end
+
+  desc 'Install gems to local directory'
+  task :bundle_install do
+    if RUBY_VERSION !~ /^2\.2\./
+      abort "You can only 'bundle install' using Ruby 2.2, because that's " \
+            'what Traveling Ruby uses.'
+    end
+
+    cd Rake.original_dir do
+      cp 'Gemfile', TMP_DIR
+      File.write("#{TMP_DIR}/#{GEMSPEC.name}.gemspec", edited_gemspec_content)
+    end
+
+    cd TMP_DIR do
+      Bundler.with_clean_env do
+        sh 'env BUNDLE_IGNORE_CONFIG=1 bundle install --path vendor ' \
+          '--without development test'
+      end
+
+      cd 'vendor/ruby/2.2.0' do
+        cd 'gems' do
+          mkdir APP_NAME
+          %w[aux lib].each { |d| cp_r "#{Rake.original_dir}/#{d}", APP_NAME }
+        end
+
+        cd 'specifications' do
+          cp "#{TMP_DIR}/#{GEMSPEC.name}.gemspec", "#{APP_NAME}.gemspec"
+        end
+      end
+
+      mkdir 'blast_db'
+      cd 'blast_db' do
+        sh 'update_blastdb.pl --decompress swissprot' do |_, e|
+          abort 'update_blastdb.pl failed to run.' if e.exitstatus == 2
+          # This script returns 0 on successful operations that result in no
+          # downloads, 1 on successful operations that downloaded files,
+          # and 2 on errors.
+        end
+      end
+    end
+  end
+
+  desc 'Reduce Vendor size'
+  task :reduce_bundle_size do
+    cd "#{TMP_DIR}/vendor" do
+      sh 'rm -f */*/cache/*'
+      sh 'rm -rf ruby/*/extensions'
+      sh "find ruby/2.2.0/gems -name '*.so' | xargs rm -f"
+      sh "find ruby/2.2.0/gems -name '*.bundle' | xargs rm -f"
+      sh "find ruby/2.2.0/gems -name '*.o' | xargs rm -f"
+
+      # Remove tests
+      %w[test tests spec features benchmark].each do |dir|
+        sh "rm -rf ruby/*/gems/*/#{dir}"
+      end
+
+      # Remove documentation
+      %w[README* CHANGE* Change* COPYING* LICENSE* MIT-LICENSE* TODO *.txt *.md *.rdoc].each do |file|
+        sh "rm -f ruby/*/gems/*/#{file}"
+      end
+      %w[doc docs example examples sample doc-api].each do |dir|
+        sh "rm -rf ruby/*/gems/*/#{dir}"
+      end
+      sh "find ruby -name '*.md' | xargs rm -f"
+
+      # Remove misc unnecessary files
+      sh 'rm -rf ruby/*/gems/*/.gitignore'
+      sh 'rm -rf ruby/*/gems/*/.travis.yml'
+
+      # Remove leftover native extension sources and compilation objects
+      sh 'rm -f ruby/*/gems/*/ext/Makefile'
+      sh 'rm -f ruby/*/gems/*/ext/*/Makefile'
+      sh 'rm -f ruby/*/gems/*/ext/*/tmp'
+      sh "find ruby -name '*.c' | xargs rm -f"
+      sh "find ruby -name '*.cpp' | xargs rm -f"
+      sh "find ruby -name '*.h' | xargs rm -f"
+      sh "find ruby -name '*.rl' | xargs rm -f"
+      sh "find ruby -name 'extconf.rb' | xargs rm -f"
+      sh "find ruby/2.2.0/gems -name '*.o' | xargs rm -f"
+      sh "find ruby/2.2.0/gems -name '*.so' | xargs rm -f"
+      sh "find ruby/2.2.0/gems -name '*.bundle' | xargs rm -f"
+
+      # Remove Java files. They're only used for JRuby support
+      sh "find ruby -name '*.java' | xargs rm -f"
+      sh "find ruby -name '*.class' | xargs rm -f"
+    end
+  end
+end
+
+PLATFORMS.each do |platform|
+  file "#{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz" do
+    download_runtime(platform)
+  end
+  file "#{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}-#{NOKOGIRI_VERSION}.tar.gz" do
+    download_native_extension(platform, NOKOGIRI_VERSION)
+  end
+end
+
+def download_runtime(platform)
+  sh "curl -L --fail -o #{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz " \
+     "https://d6r77u77i8pq3.cloudfront.net/releases/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz"
+end
+
+def download_native_extension(platform, gem_name_and_version)
+  sh "curl -L --fail -o #{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}-#{gem_name_and_version}.tar.gz " \
+     "https://d6r77u77i8pq3.cloudfront.net/releases/#{TRAVELING_RUBYGEMS_VERSION}-#{platform}/#{gem_name_and_version}.tar.gz"
+end
+
+def process_package(url, package_name)
+  if url.end_with?('.tar.gz', '.tgz')
+    mkdir package_name
+    cd package_name do
+      sh "curl -L --fail #{url} | tar -xzf - --strip-components=1"
+    end
+  elsif url.end_with?('.zip')
+    sh "curl -L --fail #{url} -o #{package_name}.zip"
+    sh "unzip #{package_name}.zip"
+    mv 'mafft-mac', package_name
+    rm "#{package_name}.zip"
+  end
+end
+
+def edited_gemspec_content
+  file_list = Dir['lib/**/**'] + Dir['aux/**/**']
+  edited_gemspec = []
+  File.readlines('genevalidator.gemspec').each_with_index do |l, index|
+    next if index < 4 # skip first four lines
+    l = "s.version = '#{GEMSPEC.version}'\n" if l =~ /^\s+s.version/
+    l = "s.files = ['#{file_list.join("','")}']\n" if l =~ /^\s+s.files/
+    l = "s.add_dependency 'nokogiri', '1.6.6.2'\nend" if l =~ /^end/
+    edited_gemspec << l
+  end
+  edited_gemspec.join
+end
+
+GEMFILE_CONTENTS = <<-GEMFILE.freeze
+source 'http://rubygems.org'
+
+gem 'bio', '~> 1.4'
+gem 'bio-blastxmlparser', '~> 2.0'
+gem '#{GEMSPEC.name}', '#{GEMSPEC.version}'
+gem 'nokogiri', '1.6.6.2'
+gem 'statsample', '2.1.0'
+GEMFILE
+
+SCRIPT_CONTENTS = <<-SCRIPT.freeze
+#!/bin/bash
+set -e
+
+# Figure out where this script is located.
+SELFDIR="$(dirname "$0")"
+SELFDIR="$(cd "$SELFDIR" && pwd)"
+
+# Tell Bundler where the Gemfile and gems are.
+export BUNDLE_GEMFILE="${SELFDIR}/lib/vendor/Gemfile"
+unset BUNDLE_IGNORE_CONFIG
+
+MAFFT_DIR="${SELFDIR}/lib/packages/mafft/mafftdir"
+BLAST_BIN="${SELFDIR}/lib/packages/blast/bin"
+GV_BLAST_DB_DIR="${SELFDIR}/blast_db"; export GV_BLAST_DB_DIR
+
+MAFFT_BINARIES="${MAFFT_DIR}/libexec"; export MAFFT_BINARIES;
+
+# Run the actual app using the bundled Ruby interpreter, with Bundler activated.
+PATH=${MAFFT_DIR}/bin:${BLAST_BIN}:$PATH  exec "${SELFDIR}/lib/ruby/bin/ruby" -rbundler/setup "${SELFDIR}/lib/app/bin/genevalidator" --db "${GV_BLAST_DB_DIR}/swissprot" "$@"
+
+SCRIPT
+
+BUNDLER_CONFIG = <<-CONFIG.freeze
+BUNDLE_PATH: .
+BUNDLE_WITHOUT: "development:test"
+BUNDLE_DISABLE_SHARED_GEMS: '1'
+CONFIG
+
+def readme_contents(platform)
+  <<-README
+
+--------------------------------------------------------------------------------
+GeneValidator (v#{GEMSPEC.version})
+Website: https://wurmlab.github.io/tools/genevalidator/
+Paper: https://doi.org/10.1093/bioinformatics/btw015
+
+Standalone Package for #{platform}.
+This package includes BLAST+ (v#{BLAST[:version]}), MAFFT (v#{MAFFT[:version]}), JQ (v#{JQ[:version]}), CSVTK (v#{CSVTK[:version]}) and the Swissprot BLAST database.
+
+Please cite as follows:
+Dragan M‡, Moghul MI‡, Priyam A, Bustos C & Wurm Y. 2015.
+GeneValidator: identify problems with protein-coding gene predictions".
+Bioinformatics, doi: 10.1093/bioinformatics/btw015.
+-------------------------------------------------------------------------------
+
+Running GeneValidator with Exemplar Data:
+
+    cd /path/to/genevalidator/package/
+    genevalidator -d blast_db/swissprot exemplar_data/protein_data.fa
+
+Run the following to see all options available.
+
+  genevalidator -h
+
+See https://github.com/wurmlab/genevalidator for more usage information.
+
+Please contact us if you require any further information.
+
+-------------------------------------------------------------------------------
+Genevalidator is licensed under the AGPL-3.0 License.
+
+Dependencies packaged with GeneValidator are licensed under their respective licenses:
+BLAST+ (Public Domain), Mafft (BSD), JQ (MIT), CSVTK (MIT) and SwissProt BLAST DB (CC BY-ND 3.0).
+-------------------------------------------------------------------------------
+
+README
+end

data/aux/gv_results.slim

@@ -0,0 +1,155 @@
+doctype html
+html
+  head
+    title GeneValidator: identify problems with gene predictions
+    script src="html_files/js/gv.compiled.min.js" type="text/javascript"
+    link href="html_files/css/gv.compiled.min.css" rel="stylesheet" type="text/css" /
+  body
+    #spinner1.modal aria-hidden="true" role="dialog" tabindex="-1"
+      .modal-dialog
+        .modal-content
+          .modal-body.text-center
+            h2 Loading ...
+            i.fa.fa-spinner.fa-5x.fa-spin
+    #alert.modal.fade aria-hidden="true" role="dialog" tabindex="-1"
+      .modal-dialog
+        .modal-content
+          .modal-header
+            button.close data-dismiss="modal" type="button"
+              span aria-hidden="true"  ×
+              span.sr-only Close
+            h4.modal-title Oops, Something went wrong!
+          .modal-body
+            p This operation is not posible. There seems to be too many queries...
+          .modal-footer
+            button.btn.btn-default data-dismiss="modal" type="button"  Close
+    #browseralert.modal.fade aria-hidden="true" role="dialog" tabindex="-1"
+      .modal-dialog
+        .modal-content.browser-alert
+          .modal-header
+            button.close data-dismiss="modal" type="button"
+              span aria-hidden="true"  ×
+              span.sr-only Close
+            h4.modal-title Incompatible Browser!
+          #browseralertbody.modal-body
+            p#browseralertText
+              strong#mainbrowseralertText Sorry, this feature is not supported in your browser.
+              br
+              strong Please run the following command in your terminal:
+              pre style="background-color: #f2dede"
+                | genevalidator serve #{@dirs[:output_dir]}
+            p This is because some browsers do not allow access to local files.
+            p
+              | Alternatively, you can use 
+              strong Mozilla FireFox 
+              | to view this file without running the above web server.
+    .container
+      span.menu_icon.pull-right
+        a href="#" onclick="GV.toggleAllPlots(this);"
+          i.fa.fa-2x.fa-bar-chart-o
+          br/
+          span#show_all_plots Show All Charts
+      span.menu_icon.pull-right
+        a href="https://github.com/wurmlab/genevalidator" target="_blank"
+          i.fa.fa-2x.fa-github
+          br/
+          | Source Code
+      span.menu_icon.pull-right
+        a href="http://wurmlab.github.io/tools/genevalidator/"
+          i.fa.fa-2x.fa-info-circle
+          br/
+          | About
+      .clearfix
+      img.logo alt="logo" src="html_files/img/gene.png" /
+      .page-title
+        h1
+          | Gene Validator
+          small
+            | v#{GeneValidator::VERSION}
+        h4.subheading Identify Problems with Gene Predictions
+      #overview.text-left style="margin-top:20px"
+        #overview_text
+        button#overview_btn.btn.btn-primary.btn-sm data-toggle="button" onclick="GV.toggleOverviewBtn();" data-overviewjson="html_files/json/overview.json"
+      - if @all_html_fnames.length > 1
+        nav
+          ul.pagination
+            - @all_html_fnames.each_with_index do |file, idx|
+              li
+                a href="#{File.basename(file)}"
+                  = idx + 1
+      table#sortable_table.table.table-striped.table-collapsed.table-bordered.table-condensed.tablesorter style="margin-top:20px"
+        thead
+          tr#header
+            th #
+            th Ranking
+            th
+              | Sequence Definition 
+              span data-placement="top" data-toggle="tooltip" title=("Query definition as it apears in the input fasta file.")
+                i.fa.fa-question-circle
+            th
+              | No. Hits 
+              span data-placement="top" data-toggle="tooltip" title=("Number of non-identical hits found by BLAST.")
+                i.fa.fa-question-circle
+            - @json_data_section[0][:validations].each do |_short_header, item|
+              th.sorter-false
+                strong
+                  = item[:header]
+                |  
+                - if item[:header] == "Length Cluster" || item[:header] == "Gene Merge" || item[:header] == "Main ORF" || item[:header] == "Missing/Extra Sequences"
+                  span data-placement="top" data-toggle="tooltip" title=("Charts available for this validation")
+                    i.fa.fa-bar-chart-o.chartIcon
+                |  
+                span data-placement="top" data-toggle="tooltip" title="#{item[:description]}"
+                  i.fa.fa-question-circle
+            th.sorter-false.chart-column
+        tbody
+          - @json_data_section.each do |row|
+            tr data-jsonfile="html_files/json/#{@dirs[:filename]}_#{row[:idx]}.json" data-target="toggle#{row[:idx]}"
+              td title="idx" = row[:idx]
+              td data-score="#{row[:overall_score]}"
+                .ratings
+                  .empty-stars
+                  .full-stars style=("width:#{row[:overall_score]}%;")
+              td title="Definition" = row[:definition]
+              td title=("No. Hits") = row[:no_hits]
+              - row[:validations].each do |_short_header, item|
+                td class="#{item[:status]}" title="#{item[:header]}"
+                  == item[:print].gsub(' ', ' ').gsub('; ', '; ')
+              - if row[:validations].select { |_short_header, item| item[:graphs] != nil }.map{ |_short_header, item| item[:graphs].length }.inject(0) { |r, e| r + e } != 0
+                td
+                  button.plot_btn.btn.btn-default title=("Show plots")
+                    i.fa.fa-bar-chart-o
+              - else
+                td
+    - if @all_html_fnames.length > 1
+      nav
+        ul.pagination
+          - @all_html_fnames.each_with_index do |file, idx|
+            li
+              a href="#{File.basename(file)}"
+                = idx + 1
+    footer
+      .container.center-block
+        p.text-muted.text-center
+          | Please cite:
+          a href="https://academic.oup.com/bioinformatics/article/32/10/1559/1742817/GeneValidator-identify-problems-with-protein" 
+            | "Dragan M
+            sup> ‡
+            | , Moghul MI
+            sup> ‡
+            | , Priyam A, Bustos C & Wurm Y
+            em (2016)
+            | GeneValidator: identify problematic gene predictions"
+          br/
+          | Developed at
+          a href="https://wurmlab.github.io" target="_blank"  Wurm Lab
+          | ,
+          a href="http://www.sbcs.qmul.ac.uk" target="_blank"  QMUL
+          | with funding by
+          a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank"  BBSRC
+          | and
+          a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank"  Google Summer of Code 2013
+          br/
+          | This page was created by 
+          a href="https://wurmlab.github.io/tools/genevalidator/" target="_blank"  GeneValidator
+          | v#{GeneValidator::VERSION}