sequenceserver 0.8.6 → 0.8.7.beta1
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- checksums.yaml +7 -0
- data/lib/profile_code.rb +217 -0
- data/lib/sequenceserver.rb +11 -8
- data/sequenceserver.gemspec +1 -1
- data/tests/test_ui.rb~ +104 -0
- metadata +80 -89
checksums.yaml
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---
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SHA1:
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metadata.gz: 497b668eaeb852effdb0181e176e37c7c8fe746f
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data.tar.gz: 1999260fc36d0d0defccbe80123f5dc85650f6a5
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SHA512:
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metadata.gz: 00b1a531ab3dae22b949581e8d2d73ef0948b12186284701dac14e90aa790f959c0b19f3c6daaa8b4d88e6f7b8fa5099fb7c632e7335b612b5bdaf1b4b17beca
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data.tar.gz: 4600be84bc18e1ac2e93f11340355a867292bcec70d6c79758a6a9d6e88b75080870fea5e39c9faeaff0029bcc20187adb2daff2e52c3a92ef119767f1e127e7
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data/lib/profile_code.rb
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@@ -0,0 +1,217 @@
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require 'ruby-prof'
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$:.unshift '.'
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#require 'sinatra/base'
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require 'yaml'
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require 'logger'
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require 'fileutils'
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require 'sequenceserver/helpers'
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require 'sequenceserver/blast'
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require 'sequenceserver/sequencehelpers'
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require 'sequenceserver/sinatralikeloggerformatter'
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require 'sequenceserver/customisation'
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require 'sequenceserver/version'
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require 'sequenceserver'
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query = '>1111883
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GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTG
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GCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACG
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22
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GCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGC
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ACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGA
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CGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGAC
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25
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TCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACG
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26
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CCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGG
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27
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CTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCG
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CGGTAATACGGAGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGTG
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29
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GCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGC
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GAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATAT
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CGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGAC
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AGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACT
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AGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGG
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GGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGA
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GCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCA
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AGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCACAGGTGCTGCATGGCTGTCGT
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CAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACTCTCGCTCCCAGT
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TGCCAGCGGTTCGGCCGGGGACTCTGGGGGGACTGCCGGCGTTAAGCCGGAGGAAGGTGG
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GGACGACGTCAAGTCATCATGGCCCTTACGTCCAGGGCGACACACGTGCTACAATGCCTG
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GTACAGCGCGTCGCGAACTCGCAAGAGGGAGCCAATCGCCAAAAGCCGGGCTAAGTTCGG
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ATTGTCGTCTGCAACTCGACGGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCCAC
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GCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGCCATGGAAGCCGGA
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GGGACCCGAAACCGGTGGGCCAACCGCAAGGGGGCAGCCGTCTAAGGT'
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#blastn -db '/home/ben/git/sequenceserver/db/97_otus.fasta' -query '/tmp/sequenceserver_query20140119-10926-qt2ecp' -task blastn -num_threads 1 -html
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method = 'blastn'#params['method']
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databases = ['/home/ben/git/sequenceserver/db/97_otus.fasta']#params[:databases]
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sequence = query #params[:sequence]
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advanced_opts = '-max_target_seqs 1'#params['advanced']
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# evaluate empty sequence as nil, otherwise as fasta
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# sequence = sequence.empty? ? nil : to_fasta(sequence)
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# blastn implies blastn, not megablast; but let's not interfere if a user
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# specifies `task` herself
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if method == 'blastn' and not advanced_opts =~ /task/
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#advanced_opts << ' -task blastn '
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end
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# run blast and log
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blast = SequenceServer::Blast.new(method, sequence, databases.join(' '), advanced_opts)
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blast.run!
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puts('Ran: ' + blast.command)
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def format_blast_results(result, databases)
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formatted_result = ''
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@all_retrievable_ids = []
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string_of_used_databases = databases.join(' ')
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blast_database_number = 0
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line_number = 0
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started_query = false
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finished_database_summary = false
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finished_alignments = false
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reference_string = ''
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database_summary_string = ''
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result.each do |line|
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line_number += 1
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next if line_number <= 5 #skip the first 5 lines
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# Add the reference to the end, not the start, of the blast result
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if line_number >= 7 and line_number <= 15
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reference_string += line
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next
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end
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if !finished_database_summary and line_number > 15
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database_summary_string += line
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finished_database_summary = true if line.match(/total letters/)
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next
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end
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# Remove certain lines from the output
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skipped_lines = [/^<\/BODY>/,/^<\/HTML>/,/^<\/PRE>/]
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skip = false
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skipped_lines.each do |skippy|
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# $stderr.puts "`#{line}' matches #{skippy}?"
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if skippy.match(line)
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skip = true
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# $stderr.puts 'yes'
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else
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# $stderr.puts 'no'
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end
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end
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next if skip
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# Remove the javascript inclusion
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line.gsub!(/^<script src=\"blastResult.js\"><\/script>/, '')
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if line.match(/^>/) # If line to possibly replace
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# Reposition the anchor to the end of the line, so that it both still works and
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# doesn't interfere with the diagnostic space at the beginning of the line.
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#
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# There are two cases:
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#
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# database formatted _with_ -parse_seqids
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line.gsub!(/^>(.+)(<a.*><\/a>)(.*)/, '>\1\3\2')
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#
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# database formatted _without_ -parse_seqids
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line.gsub!(/^>(<a.*><\/a>)(.*)/, '>\2\1')
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# get hit coordinates -- useful for linking to genome browsers
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hit_length = result[line_number..-1].index{|l| l =~ />lcl|Lambda/}
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hit_coordinates = result[line_number, hit_length].grep(/Sbjct/).
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map(&:split).map{|l| [l[1], l[-1]]}.flatten.map(&:to_i).minmax
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# Create the hyperlink (if required)
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formatted_result += construct_sequence_hyperlink_line(line, databases, hit_coordinates)
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else
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# Surround each query's result in <div> tags so they can be coloured by CSS
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if matches = line.match(/^<b>Query=<\/b> (.*)/) # If starting a new query, then surround in new <div> tag, and finish the last one off
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line = "<div class=\"resultn\" id=\"#{matches[1]}\">\n<h3>Query= #{matches[1]}</h3><pre>"
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unless blast_database_number == 0
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line = "</pre></div>\n#{line}"
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end
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blast_database_number += 1
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elsif line.match(/^ Database: /) and !finished_alignments
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formatted_result += "</div>\n<pre>#{database_summary_string}\n\n"
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finished_alignments = true
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end
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formatted_result += line
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end
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end
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formatted_result << "</pre>"
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link_to_fasta_of_all = "/get_sequence/?id=#{@all_retrievable_ids.join(' ')}&db=#{string_of_used_databases}"
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# #dbs must be sep by ' '
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retrieval_text = @all_retrievable_ids.empty? ? '' : "<a href='#{url(link_to_fasta_of_all)}'>FASTA of #{@all_retrievable_ids.length} retrievable hit(s)</a>"
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"<h2>Results</h2>"+
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retrieval_text +
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"<br/><br/>" +
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formatted_result +
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"<br/>" +
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"<pre>#{reference_string.strip}</pre>"
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end
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def construct_sequence_hyperlink_line(line, databases, hit_coordinates)
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matches = line.match(/^>(.+)/)
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sequence_id = matches[1]
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link = nil
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# If a custom sequence hyperlink method has been defined,
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# use that.
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options = {
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:sequence_id => sequence_id,
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:databases => databases,
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:hit_coordinates => hit_coordinates
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}
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# First precedence: construct the whole line to be customised
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if self.respond_to?(:construct_custom_sequence_hyperlinking_line)
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settings.log.debug("Using custom hyperlinking line creator with sequence #{options.inspect}")
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link_line = construct_custom_sequence_hyperlinking_line(options)
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unless link_line.nil?
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return link_line
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end
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end
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# If we have reached here, custom construction of the
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# whole line either wasn't defined, or returned nil
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# (indicating failure)
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if self.respond_to?(:construct_custom_sequence_hyperlink)
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# settings.log.debug("Using custom hyperlink creator with sequence #{options.inspect}")
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link = construct_custom_sequence_hyperlink(options)
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else
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# settings.log.debug("Using standard hyperlink creator with sequence `#{options.inspect}'")
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link = construct_standard_sequence_hyperlink(options)
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end
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# Return the BLAST output line with the link in it
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if link.nil?
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# settings.log.debug('No link added link for: `'+ sequence_id +'\'')
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return line
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else
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settings.log.debug('Added link for: `'+ sequence_id +'\''+ link)
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return "><a href='#{url(link)}' target='_blank'>#{sequence_id}</a> \n"
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end
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end
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# Advanced options are specified by the user. Here they are checked for interference with SequenceServer operations.
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# raise ArgumentError if an error has occurred, otherwise return without value
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def validate_advanced_parameters(advanced_options)
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raise ArgumentError, "Invalid characters detected in the advanced options" unless advanced_options =~ /\A[a-z0-9\-_\. ']*\Z/i
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disallowed_options = %w(-out -html -outfmt -db -query)
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disallowed_options.each do |o|
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raise ArgumentError, "The advanced BLAST option \"#{o}\" is used internally by SequenceServer and so cannot be specified by the you" if advanced_options =~ /#{o}/i
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end
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end
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puts format_blast_results(blast.result, databases)
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data/lib/sequenceserver.rb
CHANGED
@@ -337,8 +337,8 @@ module SequenceServer
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<em>#{found_sequences_count > sequenceids.length ? 'more' : 'less'}</em>
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sequence than expected.</strong></p>
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-
<p>This is likely due to a problem with how databases are formatted.
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-
<strong>Please share this text with the person managing this website so
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<p>This is likely due to a problem with how databases are formatted.
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<strong>Please share this text with the person managing this website so
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they can resolve the issue.</strong></p>
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<p> You requested #{sequenceids.length} sequence#{sequenceids.length > 1 ? 's' : ''}
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@@ -375,7 +375,10 @@ HEADER
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end
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def format_blast_results(result, databases)
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-
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# Constructing the result in an Array and then calling Array#join is much faster than
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# building up a String and using +=, as older versions of SeqServ did.
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formatted_results = []
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@all_retrievable_ids = []
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string_of_used_databases = databases.join(' ')
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blast_database_number = 0
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@@ -436,7 +439,7 @@ HEADER
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map(&:split).map{|l| [l[1], l[-1]]}.flatten.map(&:to_i).minmax
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# Create the hyperlink (if required)
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439
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-
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442
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formatted_results << construct_sequence_hyperlink_line(line, databases, hit_coordinates)
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else
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444
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# Surround each query's result in <div> tags so they can be coloured by CSS
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if matches = line.match(/^<b>Query=<\/b> (.*)/) # If starting a new query, then surround in new <div> tag, and finish the last one off
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@@ -446,13 +449,13 @@ HEADER
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446
449
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end
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450
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blast_database_number += 1
|
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451
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elsif line.match(/^ Database: /) and !finished_alignments
|
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-
|
452
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formatted_results << "</div>\n<pre>#{database_summary_string}\n\n"
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450
453
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finished_alignments = true
|
451
454
|
end
|
452
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-
|
455
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+
formatted_results << line
|
453
456
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end
|
454
457
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end
|
455
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-
|
458
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formatted_results << "</pre>"
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456
459
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|
457
460
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link_to_fasta_of_all = "/get_sequence/?id=#{@all_retrievable_ids.join(' ')}&db=#{string_of_used_databases}"
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461
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# #dbs must be sep by ' '
|
@@ -461,7 +464,7 @@ HEADER
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461
464
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"<h2>Results</h2>"+
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465
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retrieval_text +
|
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466
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"<br/><br/>" +
|
464
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-
|
467
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+
formatted_results.join +
|
465
468
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"<br/>" +
|
466
469
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"<pre>#{reference_string.strip}</pre>"
|
467
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end
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data/sequenceserver.gemspec
CHANGED
data/tests/test_ui.rb~
ADDED
@@ -0,0 +1,104 @@
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1
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require 'rspec'
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2
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require 'watir-webdriver'
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3
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require 'headless'
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4
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|
5
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# These shared examples should work for
|
6
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shared_examples_for 'a browser' do
|
7
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let(:seqserv_url){'http://localhost:4567'}
|
8
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|
9
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it 'should simply go the seqserv webpage' do
|
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b.goto seqserv_url
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b.url.gsub(/\/$/,'').should eq(seqserv_url)
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b.ready_state.should eq('complete')
|
13
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+
end
|
14
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|
15
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it 'should do a simple blastp' do
|
16
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b.goto seqserv_url
|
17
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|
18
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# Nucleotide database should be available
|
19
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b.checkbox(:value => 'e205221dd32dc53ebfc9fb48cbdecd9e').enabled?.should eq(true)
|
20
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+
|
21
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+
# First up the blast button should be disabled
|
22
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+
b.button(:id => 'method').text.should eq('BLAST')
|
23
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+
b.button(:id => 'method').enabled?.should eq(false)
|
24
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+
|
25
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+
# Pick a protein blast database
|
26
|
+
b.checkbox(:value => '6669b1c88665158621afc06407ce88ea').set
|
27
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+
b.checkbox(:value => '6669b1c88665158621afc06407ce88ea').checked?.should eq(true)
|
28
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+
|
29
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+
# nuc dbs now disabled
|
30
|
+
b.checkbox(:value => 'e205221dd32dc53ebfc9fb48cbdecd9e').enabled?.should eq(false)
|
31
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+
|
32
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+
# The blast button should still be disabled
|
33
|
+
b.button(:id => 'method').text.should eq('BLAST')
|
34
|
+
b.button(:id => 'method').enabled?.should eq(false)
|
35
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+
|
36
|
+
# Give a sequence we know should hit
|
37
|
+
b.textarea(:name => 'sequence').set 'YTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLA'
|
38
|
+
|
39
|
+
#blast butn now active
|
40
|
+
b.button(:id => 'method').text.should eq('BLASTP')
|
41
|
+
b.button(:id => 'method').enabled?.should eq(true)
|
42
|
+
|
43
|
+
# Run the blast
|
44
|
+
b.button(:id => 'method').click
|
45
|
+
|
46
|
+
while b.div(:id => 'result').text.include?('Waiting for BLAST to be run')
|
47
|
+
end
|
48
|
+
|
49
|
+
# blast should have worked
|
50
|
+
b.div(:id => 'result').text.include?('Sequences producing significant alignments: ').should eq(true)
|
51
|
+
end
|
52
|
+
end
|
53
|
+
|
54
|
+
#####################################################################################
|
55
|
+
#+++++++++++ Below is admin code, hopefully not necessary to mess around with to test new UI specs
|
56
|
+
|
57
|
+
# NOT thread-safe, at least because of the interaction with headless
|
58
|
+
class BrowserAdmin
|
59
|
+
def self.setup_browser(type)
|
60
|
+
case type
|
61
|
+
when :firefox then
|
62
|
+
Watir::Browser.new :firefox
|
63
|
+
when :chrome then
|
64
|
+
Watir::Browser.new :chrome
|
65
|
+
when :headless_firefox then
|
66
|
+
@headless = Headless.new
|
67
|
+
@headless.start
|
68
|
+
Watir::Browser.new :firefox
|
69
|
+
when :headless_chrome then
|
70
|
+
@headless = Headless.new
|
71
|
+
@headless.start
|
72
|
+
Watir::Browser.new :chrome
|
73
|
+
else
|
74
|
+
raise "Unknown browser type asked for: #{type.inspect}"
|
75
|
+
end
|
76
|
+
end
|
77
|
+
|
78
|
+
def self.teardown_browser(browser)
|
79
|
+
browser.close
|
80
|
+
|
81
|
+
# Re-head again, but maybe this makes no difference
|
82
|
+
@headless.destroy unless @headless.nil?
|
83
|
+
@headless = nil
|
84
|
+
end
|
85
|
+
end
|
86
|
+
|
87
|
+
|
88
|
+
describe 'ui' do
|
89
|
+
[:firefox, :chrome, :headless_firefox, :headless_chrome].each do |bro|
|
90
|
+
context bro.to_s do
|
91
|
+
it_behaves_like 'a browser' do
|
92
|
+
browser = nil
|
93
|
+
before do
|
94
|
+
browser = BrowserAdmin.setup_browser bro
|
95
|
+
end
|
96
|
+
after do
|
97
|
+
BrowserAdmin.teardown_browser browser
|
98
|
+
end
|
99
|
+
let(:b){browser}
|
100
|
+
end
|
101
|
+
end
|
102
|
+
end
|
103
|
+
end
|
104
|
+
|
metadata
CHANGED
@@ -1,8 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sequenceserver
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.8.
|
5
|
-
prerelease:
|
4
|
+
version: 0.8.7.beta1
|
6
5
|
platform: ruby
|
7
6
|
authors:
|
8
7
|
- Anurag Priyam
|
@@ -11,224 +10,216 @@ authors:
|
|
11
10
|
autorequire:
|
12
11
|
bindir: bin
|
13
12
|
cert_chain: []
|
14
|
-
date:
|
13
|
+
date: 2014-01-21 00:00:00.000000000 Z
|
15
14
|
dependencies:
|
16
15
|
- !ruby/object:Gem::Dependency
|
17
16
|
name: bundler
|
18
17
|
requirement: !ruby/object:Gem::Requirement
|
19
|
-
none: false
|
20
18
|
requirements:
|
21
|
-
- - ~>
|
19
|
+
- - "~>"
|
22
20
|
- !ruby/object:Gem::Version
|
23
21
|
version: '1.2'
|
24
22
|
type: :runtime
|
25
23
|
prerelease: false
|
26
24
|
version_requirements: !ruby/object:Gem::Requirement
|
27
|
-
none: false
|
28
25
|
requirements:
|
29
|
-
- - ~>
|
26
|
+
- - "~>"
|
30
27
|
- !ruby/object:Gem::Version
|
31
28
|
version: '1.2'
|
32
29
|
- !ruby/object:Gem::Dependency
|
33
30
|
name: sinatra
|
34
31
|
requirement: !ruby/object:Gem::Requirement
|
35
|
-
none: false
|
36
32
|
requirements:
|
37
|
-
- - ~>
|
33
|
+
- - "~>"
|
38
34
|
- !ruby/object:Gem::Version
|
39
35
|
version: 1.3.0
|
40
36
|
type: :runtime
|
41
37
|
prerelease: false
|
42
38
|
version_requirements: !ruby/object:Gem::Requirement
|
43
|
-
none: false
|
44
39
|
requirements:
|
45
|
-
- - ~>
|
40
|
+
- - "~>"
|
46
41
|
- !ruby/object:Gem::Version
|
47
42
|
version: 1.3.0
|
48
43
|
- !ruby/object:Gem::Dependency
|
49
44
|
name: ptools
|
50
45
|
requirement: !ruby/object:Gem::Requirement
|
51
|
-
none: false
|
52
46
|
requirements:
|
53
|
-
- -
|
47
|
+
- - ">="
|
54
48
|
- !ruby/object:Gem::Version
|
55
49
|
version: '0'
|
56
50
|
type: :runtime
|
57
51
|
prerelease: false
|
58
52
|
version_requirements: !ruby/object:Gem::Requirement
|
59
|
-
none: false
|
60
53
|
requirements:
|
61
|
-
- -
|
54
|
+
- - ">="
|
62
55
|
- !ruby/object:Gem::Version
|
63
56
|
version: '0'
|
64
57
|
- !ruby/object:Gem::Dependency
|
65
58
|
name: minitest
|
66
59
|
requirement: !ruby/object:Gem::Requirement
|
67
|
-
none: false
|
68
60
|
requirements:
|
69
|
-
- -
|
61
|
+
- - ">="
|
70
62
|
- !ruby/object:Gem::Version
|
71
63
|
version: '0'
|
72
64
|
type: :development
|
73
65
|
prerelease: false
|
74
66
|
version_requirements: !ruby/object:Gem::Requirement
|
75
|
-
none: false
|
76
67
|
requirements:
|
77
|
-
- -
|
68
|
+
- - ">="
|
78
69
|
- !ruby/object:Gem::Version
|
79
70
|
version: '0'
|
80
71
|
- !ruby/object:Gem::Dependency
|
81
72
|
name: rack-test
|
82
73
|
requirement: !ruby/object:Gem::Requirement
|
83
|
-
none: false
|
84
74
|
requirements:
|
85
|
-
- -
|
75
|
+
- - ">="
|
86
76
|
- !ruby/object:Gem::Version
|
87
77
|
version: '0'
|
88
78
|
type: :development
|
89
79
|
prerelease: false
|
90
80
|
version_requirements: !ruby/object:Gem::Requirement
|
91
|
-
none: false
|
92
81
|
requirements:
|
93
|
-
- -
|
82
|
+
- - ">="
|
94
83
|
- !ruby/object:Gem::Version
|
95
84
|
version: '0'
|
96
85
|
- !ruby/object:Gem::Dependency
|
97
86
|
name: watir-webdriver
|
98
87
|
requirement: !ruby/object:Gem::Requirement
|
99
|
-
none: false
|
100
88
|
requirements:
|
101
|
-
- -
|
89
|
+
- - ">="
|
102
90
|
- !ruby/object:Gem::Version
|
103
91
|
version: '0'
|
104
92
|
type: :development
|
105
93
|
prerelease: false
|
106
94
|
version_requirements: !ruby/object:Gem::Requirement
|
107
|
-
none: false
|
108
95
|
requirements:
|
109
|
-
- -
|
96
|
+
- - ">="
|
110
97
|
- !ruby/object:Gem::Version
|
111
98
|
version: '0'
|
112
99
|
- !ruby/object:Gem::Dependency
|
113
100
|
name: headless
|
114
101
|
requirement: !ruby/object:Gem::Requirement
|
115
|
-
none: false
|
116
102
|
requirements:
|
117
|
-
- -
|
103
|
+
- - ">="
|
118
104
|
- !ruby/object:Gem::Version
|
119
105
|
version: '0'
|
120
106
|
type: :development
|
121
107
|
prerelease: false
|
122
108
|
version_requirements: !ruby/object:Gem::Requirement
|
123
|
-
none: false
|
124
109
|
requirements:
|
125
|
-
- -
|
110
|
+
- - ">="
|
126
111
|
- !ruby/object:Gem::Version
|
127
112
|
version: '0'
|
128
113
|
- !ruby/object:Gem::Dependency
|
129
114
|
name: rspec
|
130
115
|
requirement: !ruby/object:Gem::Requirement
|
131
|
-
none: false
|
132
116
|
requirements:
|
133
|
-
- -
|
117
|
+
- - ">="
|
134
118
|
- !ruby/object:Gem::Version
|
135
119
|
version: '0'
|
136
120
|
type: :development
|
137
121
|
prerelease: false
|
138
122
|
version_requirements: !ruby/object:Gem::Requirement
|
139
|
-
none: false
|
140
123
|
requirements:
|
141
|
-
- -
|
124
|
+
- - ">="
|
142
125
|
- !ruby/object:Gem::Version
|
143
126
|
version: '0'
|
144
|
-
description:
|
145
|
-
user interface for use locally or over the web.
|
146
|
-
|
147
|
-
'
|
127
|
+
description: |
|
128
|
+
SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
|
148
129
|
email: anurag08priyam@gmail.com
|
149
130
|
executables:
|
150
131
|
- sequenceserver
|
151
132
|
extensions: []
|
152
133
|
extra_rdoc_files: []
|
153
134
|
files:
|
154
|
-
-
|
155
|
-
-
|
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
|
156
144
|
- lib/sequenceserver/blast.rb
|
145
|
+
- lib/sequenceserver/customisation.rb
|
157
146
|
- lib/sequenceserver/database.rb
|
158
|
-
- lib/sequenceserver/
|
147
|
+
- lib/sequenceserver/database_formatter.rb
|
159
148
|
- lib/sequenceserver/helpers.rb
|
149
|
+
- lib/sequenceserver/sequencehelpers.rb
|
160
150
|
- lib/sequenceserver/sinatralikeloggerformatter.rb
|
161
|
-
- lib/sequenceserver/
|
162
|
-
-
|
163
|
-
-
|
164
|
-
-
|
165
|
-
- views/search.erb
|
166
|
-
- public/js/jquery.activity.js
|
167
|
-
- public/js/sequenceserver.js
|
168
|
-
- public/js/jquery.js
|
169
|
-
- public/js/jquery-scrollspy.js
|
170
|
-
- public/js/sequenceserver.blast.js
|
171
|
-
- public/js/bootstrap.dropdown.js
|
172
|
-
- public/js/store.min.js
|
173
|
-
- public/js/bootstrap.modal.js
|
174
|
-
- public/js/bootstrap.transition.js
|
175
|
-
- public/js/jquery-ui.js
|
176
|
-
- public/js/jquery.enablePlaceholder.min.js
|
151
|
+
- lib/sequenceserver/version.rb
|
152
|
+
- public/css/beige.css.css
|
153
|
+
- public/css/bootstrap.dropdown.css
|
154
|
+
- public/css/bootstrap.icons.css
|
177
155
|
- public/css/bootstrap.min.css
|
178
156
|
- public/css/bootstrap.modal.css
|
179
|
-
- public/css/bootstrap.icons.css
|
180
|
-
- public/css/bootstrap.dropdown.css
|
181
|
-
- public/css/beige.css.css
|
182
157
|
- public/css/custom.css
|
183
158
|
- public/img/glyphicons-halflings-white.png
|
184
159
|
- public/img/glyphicons-halflings.png
|
185
|
-
-
|
186
|
-
-
|
187
|
-
-
|
188
|
-
-
|
189
|
-
-
|
190
|
-
-
|
191
|
-
-
|
192
|
-
-
|
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
|
193
173
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
|
194
174
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
|
195
175
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
|
196
|
-
- tests/database/
|
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
|
197
180
|
- tests/run
|
198
|
-
-
|
199
|
-
-
|
200
|
-
-
|
201
|
-
-
|
202
|
-
-
|
203
|
-
-
|
204
|
-
-
|
205
|
-
-
|
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
|
206
189
|
homepage: http://sequenceserver.com
|
207
190
|
licenses:
|
208
191
|
- SequenceServer (custom)
|
209
|
-
|
210
|
-
|
211
|
-
|
212
|
-
|
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
|
+
|
213
206
|
rdoc_options: []
|
214
207
|
require_paths:
|
215
208
|
- lib
|
216
209
|
required_ruby_version: !ruby/object:Gem::Requirement
|
217
|
-
none: false
|
218
210
|
requirements:
|
219
|
-
- -
|
211
|
+
- - ">="
|
220
212
|
- !ruby/object:Gem::Version
|
221
213
|
version: '0'
|
222
214
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
223
|
-
none: false
|
224
215
|
requirements:
|
225
|
-
- -
|
216
|
+
- - ">"
|
226
217
|
- !ruby/object:Gem::Version
|
227
|
-
version:
|
218
|
+
version: 1.3.1
|
228
219
|
requirements: []
|
229
220
|
rubyforge_project:
|
230
|
-
rubygems_version:
|
221
|
+
rubygems_version: 2.2.0.rc.1
|
231
222
|
signing_key:
|
232
|
-
specification_version:
|
223
|
+
specification_version: 4
|
233
224
|
summary: BLAST search made easy!
|
234
225
|
test_files: []
|