sequenceserver-beta 0.8.7.beta1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/Gemfile +3 -0
- data/LICENSE.Apache.txt +176 -0
- data/LICENSE.txt +69 -0
- data/README.txt +5 -0
- data/bin/sequenceserver +82 -0
- data/config.ru +6 -0
- data/example.config.yml +39 -0
- data/lib/profile_code.rb +217 -0
- data/lib/sequenceserver.rb +527 -0
- data/lib/sequenceserver/blast.rb +92 -0
- data/lib/sequenceserver/customisation.rb +60 -0
- data/lib/sequenceserver/database.rb +29 -0
- data/lib/sequenceserver/database_formatter.rb +190 -0
- data/lib/sequenceserver/helpers.rb +136 -0
- data/lib/sequenceserver/sequencehelpers.rb +93 -0
- data/lib/sequenceserver/sinatralikeloggerformatter.rb +12 -0
- data/lib/sequenceserver/version.rb +9 -0
- data/public/css/beige.css.css +254 -0
- data/public/css/bootstrap.dropdown.css +29 -0
- data/public/css/bootstrap.icons.css +155 -0
- data/public/css/bootstrap.min.css +415 -0
- data/public/css/bootstrap.modal.css +28 -0
- data/public/css/custom.css +232 -0
- data/public/img/glyphicons-halflings-white.png +0 -0
- data/public/img/glyphicons-halflings.png +0 -0
- data/public/js/bootstrap.dropdown.js +92 -0
- data/public/js/bootstrap.modal.js +7 -0
- data/public/js/bootstrap.transition.js +7 -0
- data/public/js/jquery-scrollspy.js +98 -0
- data/public/js/jquery-ui.js +14987 -0
- data/public/js/jquery.activity.js +10 -0
- data/public/js/jquery.enablePlaceholder.min.js +10 -0
- data/public/js/jquery.js +5 -0
- data/public/js/sequenceserver.blast.js +208 -0
- data/public/js/sequenceserver.js +304 -0
- data/public/js/store.min.js +2 -0
- data/sequenceserver.gemspec +49 -0
- data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
- data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
- data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
- data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
- data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta +6449 -0
- data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
- data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
- data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
- data/tests/run +26 -0
- data/tests/test_sequencehelpers.rb +77 -0
- data/tests/test_sequenceserver_blast.rb +60 -0
- data/tests/test_ui.rb +104 -0
- data/tests/test_ui.rb~ +104 -0
- data/tests/ui.specs.todo +10 -0
- data/views/500.erb +22 -0
- data/views/_options.erb +144 -0
- data/views/search.erb +220 -0
- metadata +226 -0
data/views/search.erb
ADDED
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<title>SequenceServer: Custom BLAST Server</title>
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<meta name="author" content="Anurag Priyam" />
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<meta name="author" content="Ben J. Woodcroft" />
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<meta name="author" content="Yannick Wurm" />
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<meta name="author" content="Cedric Wurm" />
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<meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
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<meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
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<script type="text/javascript" src="<%= uri('/js/store.min.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/jquery-ui.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/jquery-scrollspy.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/bootstrap.transition.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/bootstrap.dropdown.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/bootstrap.modal.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/sequenceserver.js') %>"></script>
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<script type="text/javascript" src="<%= uri('/js/sequenceserver.blast.js') %>"></script>
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<%# without a space after erb's closing tag, a / gets appended to css' path %>
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<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.min.css') %>" />
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<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.dropdown.css') %>" />
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<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.modal.css') %>" />
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<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.icons.css') %>" />
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<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/custom.css') %>" />
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</head>
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<body>
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<div class="container">
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<noscript>
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<div class="nojs-error">
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<h3>SequenceServer can't work without JavaScript.</h3>
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<ul>
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<li>Please see if you can enable JavaScript in your browser's preferences.</li>
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<li>If your browser doesn't support JavaScript, please consider upgrading to the latest version or using Firefox or Chrome.</li>
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</ul>
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</div>
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</noscript>
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<div class="page">
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<div id="banner">
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<h1>BLAST Sequence(s)</h1>
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</div>
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<form method="post" id="blast" action="<%= uri('/#result') %>">
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<div class="row">
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<div class="span16">
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<div class="control-group">
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<textarea name="sequence" id="sequence" spellcheck="false" autofocus="true" placeholder="Paste your sequence(s) here..." ></textarea>
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</div>
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</div>
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</div>
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<div class="notifications">
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<div class="notification alert-info hide" id="nucleotide-sequence-notification">
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Detected: nucleotide sequence(s).
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</div>
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<div class="notification alert-info hide" id="protein-sequence-notification">
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Detected: protein sequence(s).
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</div>
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<div class="notification alert-error hide" id="mixed-sequence-notification">
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Detected: mixed nucleotide and protein sequences. We can't handle that. Please try one sequence at a time.
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</div>
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</div>
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<br class="large"/>
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<div class="row">
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<div class="span8">
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<div class="offset-left box databases nucleotide">
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<div class="clearfix">
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<fieldset>
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<legend>Nucleotide databases</legend>
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<div class="controls offset-left">
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<% settings.databases.values.select{|database| database.type == :nucleotide}.sort.each do |database| %>
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<label class="checkbox">
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<input type="checkbox" name="databases[]" value="<%=database.hash%>" data-type="<%=database.type%>" />
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<span> <%= database.title or database.name %></span>
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</label>
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<% end %>
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</div>
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</fieldset>
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</div>
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</div>
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</div>
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<div class="span8">
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<div class="offset-right box databases protein">
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<div class="clearfix">
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<fieldset>
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<legend>Protein databases</legend>
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<div class="controls offset-left">
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<% settings.databases.values.select{|database| database.type == :protein}.sort.each do |database| %>
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<label class="checkbox">
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<input type="checkbox" name="databases[]" value="<%=database.hash%>" data-type="<%=database.type%>" />
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<span> <%= database.title or database.name %></span>
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</label>
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<% end %>
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</div>
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</fieldset>
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</div>
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</div>
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</div>
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</div>
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<br class="large"/>
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<div class="row">
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<div class="span12">
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<div class="offset-left box advanced">
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<div class="clearfix">
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<label for="advanced">Advanced Parameters:</label>
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<input class="span8" type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
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<span class="icon-question-sign" data-toggle="modal" href="#help"></span>
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</div>
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<div class="modal hide fade" id="help">
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<div class="modal-header">
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<h3>Advanced Options</h3>
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</div>
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<div class="modal-body">
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<%= erb :_options %>
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</div>
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<div class="modal-footer">
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<button class="btn btn-primary" data-dismiss="modal">Got it!</button>
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</div>
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</div>
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</div>
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</div>
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<div class="span4">
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<div id="methods">
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<button type="submit" class="span3 btn btn-large btn-primary" id="method" disabled="disabled">blast</button>
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<button class="btn btn-primary btn-large dropdown-toggle hide" data-toggle="dropdown">
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<span class="caret"></span>
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</button>
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<ul class="dropdown-menu"></ul>
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</div>
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</div>
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</div>
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</form>
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<div class="modal hide" id="spinner" data-keyboard="false" data-backdrop="static">
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<div class="modal-body">
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</div>
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</div>
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<div class="results hide">
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<div id="result">Waiting for BLAST to be run <!-- need bit before for UI testing so it knows when BLAST is finished -->
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</div>
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</div>
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<div class="modal hide fade" id="error">
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<div class="modal-header">
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<h3 id="error-short">Oops! BLAST Failed</h3>
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</div>
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<div class="modal-body">
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<h4 id="error-type"></h4>
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<br/>
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<p id="error-message"></p>
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</div>
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<div class="modal-footer">
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<button class="btn btn-danger" data-dismiss="modal">Close</button>
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</div>
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</div>
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<div id="underbar">
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<p><strong><a href='http://www.sequenceserver.com'>
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<%= [ "© SequenceServer: BLAST search made easy!",
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"Custom BLAST web interface by SequenceServer.",
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"SequenceServer: Local BLAST with bespoke html interface.",
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"Set up custom BLAST interface with SequenceServer.",
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"Please cite: Priyam A, Woodcroft BJ, Wurm Y (<em>in prep</em>). " +
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"Sequenceserver: BLAST searching made easy."
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][rand(5)]
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%>
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</a></strong></p>
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</div>
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</div> <!-- /page -->
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</div> <!-- /container -->
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<div id="social" class="modal hide fade">
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<div class="modal-header">
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<h3 id="error-short">Looks like you are fond of SequenceServer :).</h3>
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</div>
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<div class="modal-body">
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<p>Please consider giving us a plus-one and/or tweeting about us. Thanks!</p>
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<br/>
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<div class="buttons">
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<div class="button-container well">
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<div class="g-plusone" data-annotation="none" data-href="http://www.sequenceserver.com"></div>
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</div>
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<div class="button-container well">
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<a href="https://twitter.com/share" class="twitter-share-button" data-url="http://www.sequenceserver.com" data-text="SequenceServer: BLAST search made easy." data-via="yeban" data-size="large" data-count="none" data-hashtags="bioinformatics">Tweet</a>
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</div>
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</div>
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</div>
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<div class="modal-footer">
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<button class="btn btn-primary" data-dismiss="modal">Done</button>
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</div>
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</div> <!-- /social -->
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<!-- google plus -->
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<script type="text/javascript">
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(function() {
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var po = document.createElement('script'); po.type = 'text/javascript'; po.async = true;
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po.src = 'https://apis.google.com/js/plusone.js';
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var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(po, s);
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})();
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</script>
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<!-- twitter -->
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<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
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</body>
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</html>
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metadata
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--- !ruby/object:Gem::Specification
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name: sequenceserver-beta
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version: !ruby/object:Gem::Version
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version: 0.8.7.beta1
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platform: ruby
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authors:
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- Anurag Priyam
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- Ben J Woodcroft
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- Yannick Wurm
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-01-21 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.2'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.2'
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- !ruby/object:Gem::Dependency
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name: sinatra
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 1.3.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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40
|
+
- - "~>"
|
|
41
|
+
- !ruby/object:Gem::Version
|
|
42
|
+
version: 1.3.0
|
|
43
|
+
- !ruby/object:Gem::Dependency
|
|
44
|
+
name: ptools
|
|
45
|
+
requirement: !ruby/object:Gem::Requirement
|
|
46
|
+
requirements:
|
|
47
|
+
- - ">="
|
|
48
|
+
- !ruby/object:Gem::Version
|
|
49
|
+
version: '0'
|
|
50
|
+
type: :runtime
|
|
51
|
+
prerelease: false
|
|
52
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
53
|
+
requirements:
|
|
54
|
+
- - ">="
|
|
55
|
+
- !ruby/object:Gem::Version
|
|
56
|
+
version: '0'
|
|
57
|
+
- !ruby/object:Gem::Dependency
|
|
58
|
+
name: minitest
|
|
59
|
+
requirement: !ruby/object:Gem::Requirement
|
|
60
|
+
requirements:
|
|
61
|
+
- - ">="
|
|
62
|
+
- !ruby/object:Gem::Version
|
|
63
|
+
version: '0'
|
|
64
|
+
type: :development
|
|
65
|
+
prerelease: false
|
|
66
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
67
|
+
requirements:
|
|
68
|
+
- - ">="
|
|
69
|
+
- !ruby/object:Gem::Version
|
|
70
|
+
version: '0'
|
|
71
|
+
- !ruby/object:Gem::Dependency
|
|
72
|
+
name: rack-test
|
|
73
|
+
requirement: !ruby/object:Gem::Requirement
|
|
74
|
+
requirements:
|
|
75
|
+
- - ">="
|
|
76
|
+
- !ruby/object:Gem::Version
|
|
77
|
+
version: '0'
|
|
78
|
+
type: :development
|
|
79
|
+
prerelease: false
|
|
80
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
81
|
+
requirements:
|
|
82
|
+
- - ">="
|
|
83
|
+
- !ruby/object:Gem::Version
|
|
84
|
+
version: '0'
|
|
85
|
+
- !ruby/object:Gem::Dependency
|
|
86
|
+
name: watir-webdriver
|
|
87
|
+
requirement: !ruby/object:Gem::Requirement
|
|
88
|
+
requirements:
|
|
89
|
+
- - ">="
|
|
90
|
+
- !ruby/object:Gem::Version
|
|
91
|
+
version: '0'
|
|
92
|
+
type: :development
|
|
93
|
+
prerelease: false
|
|
94
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
95
|
+
requirements:
|
|
96
|
+
- - ">="
|
|
97
|
+
- !ruby/object:Gem::Version
|
|
98
|
+
version: '0'
|
|
99
|
+
- !ruby/object:Gem::Dependency
|
|
100
|
+
name: headless
|
|
101
|
+
requirement: !ruby/object:Gem::Requirement
|
|
102
|
+
requirements:
|
|
103
|
+
- - ">="
|
|
104
|
+
- !ruby/object:Gem::Version
|
|
105
|
+
version: '0'
|
|
106
|
+
type: :development
|
|
107
|
+
prerelease: false
|
|
108
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
109
|
+
requirements:
|
|
110
|
+
- - ">="
|
|
111
|
+
- !ruby/object:Gem::Version
|
|
112
|
+
version: '0'
|
|
113
|
+
- !ruby/object:Gem::Dependency
|
|
114
|
+
name: rspec
|
|
115
|
+
requirement: !ruby/object:Gem::Requirement
|
|
116
|
+
requirements:
|
|
117
|
+
- - ">="
|
|
118
|
+
- !ruby/object:Gem::Version
|
|
119
|
+
version: '0'
|
|
120
|
+
type: :development
|
|
121
|
+
prerelease: false
|
|
122
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
123
|
+
requirements:
|
|
124
|
+
- - ">="
|
|
125
|
+
- !ruby/object:Gem::Version
|
|
126
|
+
version: '0'
|
|
127
|
+
description: |
|
|
128
|
+
SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
|
|
129
|
+
email: anurag08priyam@gmail.com
|
|
130
|
+
executables:
|
|
131
|
+
- sequenceserver
|
|
132
|
+
extensions: []
|
|
133
|
+
extra_rdoc_files: []
|
|
134
|
+
files:
|
|
135
|
+
- Gemfile
|
|
136
|
+
- LICENSE.Apache.txt
|
|
137
|
+
- LICENSE.txt
|
|
138
|
+
- README.txt
|
|
139
|
+
- bin/sequenceserver
|
|
140
|
+
- config.ru
|
|
141
|
+
- example.config.yml
|
|
142
|
+
- lib/profile_code.rb
|
|
143
|
+
- lib/sequenceserver.rb
|
|
144
|
+
- lib/sequenceserver/blast.rb
|
|
145
|
+
- lib/sequenceserver/customisation.rb
|
|
146
|
+
- lib/sequenceserver/database.rb
|
|
147
|
+
- lib/sequenceserver/database_formatter.rb
|
|
148
|
+
- lib/sequenceserver/helpers.rb
|
|
149
|
+
- lib/sequenceserver/sequencehelpers.rb
|
|
150
|
+
- lib/sequenceserver/sinatralikeloggerformatter.rb
|
|
151
|
+
- lib/sequenceserver/version.rb
|
|
152
|
+
- public/css/beige.css.css
|
|
153
|
+
- public/css/bootstrap.dropdown.css
|
|
154
|
+
- public/css/bootstrap.icons.css
|
|
155
|
+
- public/css/bootstrap.min.css
|
|
156
|
+
- public/css/bootstrap.modal.css
|
|
157
|
+
- public/css/custom.css
|
|
158
|
+
- public/img/glyphicons-halflings-white.png
|
|
159
|
+
- public/img/glyphicons-halflings.png
|
|
160
|
+
- public/js/bootstrap.dropdown.js
|
|
161
|
+
- public/js/bootstrap.modal.js
|
|
162
|
+
- public/js/bootstrap.transition.js
|
|
163
|
+
- public/js/jquery-scrollspy.js
|
|
164
|
+
- public/js/jquery-ui.js
|
|
165
|
+
- public/js/jquery.activity.js
|
|
166
|
+
- public/js/jquery.enablePlaceholder.min.js
|
|
167
|
+
- public/js/jquery.js
|
|
168
|
+
- public/js/sequenceserver.blast.js
|
|
169
|
+
- public/js/sequenceserver.js
|
|
170
|
+
- public/js/store.min.js
|
|
171
|
+
- sequenceserver.gemspec
|
|
172
|
+
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
|
|
173
|
+
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
|
|
174
|
+
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
|
|
175
|
+
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
|
|
176
|
+
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
|
|
177
|
+
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
|
|
178
|
+
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
|
|
179
|
+
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
|
|
180
|
+
- tests/run
|
|
181
|
+
- tests/test_sequencehelpers.rb
|
|
182
|
+
- tests/test_sequenceserver_blast.rb
|
|
183
|
+
- tests/test_ui.rb
|
|
184
|
+
- tests/test_ui.rb~
|
|
185
|
+
- tests/ui.specs.todo
|
|
186
|
+
- views/500.erb
|
|
187
|
+
- views/_options.erb
|
|
188
|
+
- views/search.erb
|
|
189
|
+
homepage: http://sequenceserver.com
|
|
190
|
+
licenses:
|
|
191
|
+
- SequenceServer (custom)
|
|
192
|
+
metadata: {}
|
|
193
|
+
post_install_message: |2+
|
|
194
|
+
|
|
195
|
+
------------------------------------------------------------------------
|
|
196
|
+
Thank you for installing SequenceServer :)!
|
|
197
|
+
|
|
198
|
+
To launch SequenceServer execute 'sequenceserver' from command line.
|
|
199
|
+
|
|
200
|
+
$ sequenceserver
|
|
201
|
+
|
|
202
|
+
|
|
203
|
+
Visit http://sequenceserver.com for more.
|
|
204
|
+
------------------------------------------------------------------------
|
|
205
|
+
|
|
206
|
+
rdoc_options: []
|
|
207
|
+
require_paths:
|
|
208
|
+
- lib
|
|
209
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
|
210
|
+
requirements:
|
|
211
|
+
- - ">="
|
|
212
|
+
- !ruby/object:Gem::Version
|
|
213
|
+
version: '0'
|
|
214
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
215
|
+
requirements:
|
|
216
|
+
- - ">"
|
|
217
|
+
- !ruby/object:Gem::Version
|
|
218
|
+
version: 1.3.1
|
|
219
|
+
requirements: []
|
|
220
|
+
rubyforge_project:
|
|
221
|
+
rubygems_version: 2.2.0.rc.1
|
|
222
|
+
signing_key:
|
|
223
|
+
specification_version: 4
|
|
224
|
+
summary: BLAST search made easy!
|
|
225
|
+
test_files: []
|
|
226
|
+
has_rdoc:
|