neurohmmerapp 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +24 -0
- data/Gemfile +4 -0
- data/Gemfile.lock +81 -0
- data/LICENSE.txt +661 -0
- data/README.md +96 -0
- data/Rakefile +21 -0
- data/bin/neurohmmerapp +166 -0
- data/config.ru +3 -0
- data/lib/neurohmmerapp/config.rb +87 -0
- data/lib/neurohmmerapp/exceptions.rb +77 -0
- data/lib/neurohmmerapp/logger.rb +24 -0
- data/lib/neurohmmerapp/neurohmmer.rb +158 -0
- data/lib/neurohmmerapp/routes.rb +79 -0
- data/lib/neurohmmerapp/server.rb +63 -0
- data/lib/neurohmmerapp/version.rb +3 -0
- data/lib/neurohmmerapp.rb +207 -0
- data/neurohmmerapp.gemspec +50 -0
- data/public/NeuroHmmer/loading.html +12 -0
- data/public/src/css/bootstrap1.min.css +7 -0
- data/public/src/css/custom.css +189 -0
- data/public/src/css/custom.min.css +1 -0
- data/public/src/css/font-awesome.min.css +4 -0
- data/public/src/js/bionode-seq.min.js +1 -0
- data/public/src/js/bootstrap.min.js +6 -0
- data/public/src/js/jquery.cookie.min.js +1 -0
- data/public/src/js/jquery.min.js +4 -0
- data/public/src/js/jquery.validate.min.js +4 -0
- data/public/src/js/neurohmmer.js +228 -0
- data/public/src/js/neurohmmer.min.js +1 -0
- data/public/web_files/css/nh_compiled_css.min.css +14 -0
- data/public/web_files/fonts/FontAwesome.otf +0 -0
- data/public/web_files/fonts/fontawesome-webfont.eot +0 -0
- data/public/web_files/fonts/fontawesome-webfont.svg +504 -0
- data/public/web_files/fonts/fontawesome-webfont.ttf +0 -0
- data/public/web_files/fonts/fontawesome-webfont.woff +0 -0
- data/public/web_files/js/nh_compiled_js.min.js +20 -0
- data/spec/empty_config.yml +0 -0
- data/spec/route_spec.rb +72 -0
- data/views/500.slim +5 -0
- data/views/index.slim +38 -0
- data/views/layout.slim +74 -0
- data/views/results.slim +9 -0
- metadata +281 -0
metadata
ADDED
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@@ -0,0 +1,281 @@
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1
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--- !ruby/object:Gem::Specification
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2
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name: neurohmmerapp
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3
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version: !ruby/object:Gem::Version
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4
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version: 0.0.1
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5
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platform: ruby
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6
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authors:
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7
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- Ismail Moghul
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8
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- Yannick Wurm
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9
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autorequire:
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10
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bindir: bin
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11
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cert_chain: []
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12
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date: 2015-11-17 00:00:00.000000000 Z
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13
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dependencies:
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14
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- !ruby/object:Gem::Dependency
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15
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name: bundler
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16
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requirement: !ruby/object:Gem::Requirement
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17
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requirements:
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18
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- - "~>"
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19
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- !ruby/object:Gem::Version
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20
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version: '1.6'
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21
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type: :development
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22
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prerelease: false
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23
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version_requirements: !ruby/object:Gem::Requirement
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24
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requirements:
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25
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+
- - "~>"
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26
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- !ruby/object:Gem::Version
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27
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version: '1.6'
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28
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+
- !ruby/object:Gem::Dependency
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29
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name: rake
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30
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requirement: !ruby/object:Gem::Requirement
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31
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requirements:
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32
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+
- - "~>"
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33
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+
- !ruby/object:Gem::Version
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34
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version: '10.3'
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35
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type: :development
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36
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+
prerelease: false
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37
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+
version_requirements: !ruby/object:Gem::Requirement
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38
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requirements:
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39
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- - "~>"
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40
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+
- !ruby/object:Gem::Version
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41
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version: '10.3'
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42
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- !ruby/object:Gem::Dependency
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43
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name: rspec
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44
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requirement: !ruby/object:Gem::Requirement
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45
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requirements:
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46
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- - "~>"
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47
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+
- !ruby/object:Gem::Version
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48
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version: '2.8'
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49
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- - ">="
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50
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- !ruby/object:Gem::Version
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51
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version: 2.8.0
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52
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type: :development
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53
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prerelease: false
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54
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version_requirements: !ruby/object:Gem::Requirement
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55
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requirements:
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56
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- - "~>"
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57
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- !ruby/object:Gem::Version
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58
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version: '2.8'
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59
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- - ">="
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60
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- !ruby/object:Gem::Version
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61
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version: 2.8.0
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62
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- !ruby/object:Gem::Dependency
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63
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name: rack-test
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64
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requirement: !ruby/object:Gem::Requirement
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65
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requirements:
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66
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- - "~>"
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67
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- !ruby/object:Gem::Version
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68
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version: '0.6'
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69
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type: :development
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70
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prerelease: false
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71
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version_requirements: !ruby/object:Gem::Requirement
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72
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requirements:
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73
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- - "~>"
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74
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- !ruby/object:Gem::Version
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75
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version: '0.6'
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76
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+
- !ruby/object:Gem::Dependency
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77
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name: capybara
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78
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requirement: !ruby/object:Gem::Requirement
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79
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requirements:
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80
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- - "~>"
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81
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- !ruby/object:Gem::Version
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82
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version: '2.4'
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83
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- - ">="
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84
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- !ruby/object:Gem::Version
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85
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version: 2.4.4
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86
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type: :development
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87
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prerelease: false
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88
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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90
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- - "~>"
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91
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- !ruby/object:Gem::Version
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92
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version: '2.4'
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93
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- - ">="
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94
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- !ruby/object:Gem::Version
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95
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version: 2.4.4
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96
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- !ruby/object:Gem::Dependency
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97
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name: w3c_validators
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98
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requirement: !ruby/object:Gem::Requirement
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99
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requirements:
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100
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- - "~>"
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101
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- !ruby/object:Gem::Version
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102
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version: '1.1'
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103
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type: :development
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104
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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106
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requirements:
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107
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- - "~>"
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108
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- !ruby/object:Gem::Version
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version: '1.1'
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- !ruby/object:Gem::Dependency
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111
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name: neurohmmer
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112
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requirement: !ruby/object:Gem::Requirement
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113
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requirements:
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114
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- - "~>"
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115
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- !ruby/object:Gem::Version
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116
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version: '0.1'
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117
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type: :runtime
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118
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prerelease: false
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119
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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121
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- - "~>"
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122
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- !ruby/object:Gem::Version
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123
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version: '0.1'
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124
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- !ruby/object:Gem::Dependency
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125
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name: bio
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126
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requirement: !ruby/object:Gem::Requirement
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127
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requirements:
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128
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- - "~>"
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129
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- !ruby/object:Gem::Version
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130
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version: '1.4'
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131
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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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134
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requirements:
|
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135
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+
- - "~>"
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136
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- !ruby/object:Gem::Version
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137
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version: '1.4'
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138
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- !ruby/object:Gem::Dependency
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139
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name: sinatra
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140
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requirement: !ruby/object:Gem::Requirement
|
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141
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requirements:
|
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142
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- - "~>"
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143
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- !ruby/object:Gem::Version
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144
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version: '1.4'
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145
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type: :runtime
|
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146
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prerelease: false
|
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147
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version_requirements: !ruby/object:Gem::Requirement
|
|
148
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requirements:
|
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149
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+
- - "~>"
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150
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- !ruby/object:Gem::Version
|
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151
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version: '1.4'
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152
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- !ruby/object:Gem::Dependency
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153
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name: sinatra-cross_origin
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154
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requirement: !ruby/object:Gem::Requirement
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155
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requirements:
|
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156
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- - "~>"
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157
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- !ruby/object:Gem::Version
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158
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version: '0.3'
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159
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type: :runtime
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160
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prerelease: false
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161
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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163
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- - "~>"
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164
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- !ruby/object:Gem::Version
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165
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version: '0.3'
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166
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- !ruby/object:Gem::Dependency
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167
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name: slim
|
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168
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requirement: !ruby/object:Gem::Requirement
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169
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requirements:
|
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170
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- - "~>"
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171
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- !ruby/object:Gem::Version
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172
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version: '3.0'
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173
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type: :runtime
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174
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prerelease: false
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175
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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178
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- !ruby/object:Gem::Version
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179
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version: '3.0'
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180
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- !ruby/object:Gem::Dependency
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181
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name: slop
|
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182
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requirement: !ruby/object:Gem::Requirement
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183
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requirements:
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184
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- - "~>"
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185
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- !ruby/object:Gem::Version
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186
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version: '3.6'
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187
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type: :runtime
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188
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prerelease: false
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189
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version_requirements: !ruby/object:Gem::Requirement
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190
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requirements:
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191
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- - "~>"
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192
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- !ruby/object:Gem::Version
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193
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version: '3.6'
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194
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description: A Web App wrapper for NeuroHmmer, a program for validating gene predictions.
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195
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email: y.wurm@qmul.ac.uk
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executables:
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197
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- neurohmmerapp
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198
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extensions: []
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199
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extra_rdoc_files: []
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files:
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201
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- ".gitignore"
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202
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- Gemfile
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203
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- Gemfile.lock
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204
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- LICENSE.txt
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205
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- README.md
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206
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- Rakefile
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207
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- bin/neurohmmerapp
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208
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- config.ru
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209
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- lib/neurohmmerapp.rb
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- lib/neurohmmerapp/config.rb
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211
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- lib/neurohmmerapp/exceptions.rb
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212
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- lib/neurohmmerapp/logger.rb
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213
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- lib/neurohmmerapp/neurohmmer.rb
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214
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- lib/neurohmmerapp/routes.rb
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215
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- lib/neurohmmerapp/server.rb
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216
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- lib/neurohmmerapp/version.rb
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217
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- neurohmmerapp.gemspec
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218
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- public/NeuroHmmer/loading.html
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219
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- public/src/css/bootstrap1.min.css
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220
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- public/src/css/custom.css
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221
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- public/src/css/custom.min.css
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222
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- public/src/css/font-awesome.min.css
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223
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- public/src/js/bionode-seq.min.js
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224
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- public/src/js/bootstrap.min.js
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225
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- public/src/js/jquery.cookie.min.js
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226
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- public/src/js/jquery.min.js
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227
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- public/src/js/jquery.validate.min.js
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228
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- public/src/js/neurohmmer.js
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229
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- public/src/js/neurohmmer.min.js
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230
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- public/web_files/css/nh_compiled_css.min.css
|
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231
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+
- public/web_files/fonts/FontAwesome.otf
|
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232
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+
- public/web_files/fonts/fontawesome-webfont.eot
|
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233
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- public/web_files/fonts/fontawesome-webfont.svg
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234
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- public/web_files/fonts/fontawesome-webfont.ttf
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235
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- public/web_files/fonts/fontawesome-webfont.woff
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236
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- public/web_files/js/nh_compiled_js.min.js
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237
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+
- spec/empty_config.yml
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238
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- spec/route_spec.rb
|
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239
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+
- views/500.slim
|
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240
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- views/index.slim
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241
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- views/layout.slim
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242
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- views/results.slim
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243
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homepage: https://github.com/wurmlab/neurohmmerapp
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244
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licenses:
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245
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- AGPL
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246
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metadata: {}
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247
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post_install_message: |2+
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248
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249
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------------------------------------------------------------------------
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|
250
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Thank you for Installing the NeuroHmmer App!
|
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251
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252
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To launch NeuroHmmerApp execute 'neurohmmerapp' from command line.
|
|
253
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254
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$ neurohmmerapp [options]
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255
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256
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Visit https://github.com/wurmlab/neurohmmerapp for more information.
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257
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------------------------------------------------------------------------
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258
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259
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rdoc_options: []
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260
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require_paths:
|
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261
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- lib
|
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262
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required_ruby_version: !ruby/object:Gem::Requirement
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263
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requirements:
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264
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- - ">="
|
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265
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- !ruby/object:Gem::Version
|
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266
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version: 2.0.0
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267
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required_rubygems_version: !ruby/object:Gem::Requirement
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268
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requirements:
|
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269
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- - ">="
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270
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- !ruby/object:Gem::Version
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271
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version: '0'
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272
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requirements: []
|
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273
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rubyforge_project:
|
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274
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rubygems_version: 2.4.8
|
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275
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signing_key:
|
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276
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specification_version: 4
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277
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summary: A Web App wrapper for NeuroHmmer.
|
|
278
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test_files:
|
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279
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+
- spec/empty_config.yml
|
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280
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- spec/route_spec.rb
|
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281
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has_rdoc:
|