neurohmmerapp 0.0.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (44) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +24 -0
  3. data/Gemfile +4 -0
  4. data/Gemfile.lock +81 -0
  5. data/LICENSE.txt +661 -0
  6. data/README.md +96 -0
  7. data/Rakefile +21 -0
  8. data/bin/neurohmmerapp +166 -0
  9. data/config.ru +3 -0
  10. data/lib/neurohmmerapp/config.rb +87 -0
  11. data/lib/neurohmmerapp/exceptions.rb +77 -0
  12. data/lib/neurohmmerapp/logger.rb +24 -0
  13. data/lib/neurohmmerapp/neurohmmer.rb +158 -0
  14. data/lib/neurohmmerapp/routes.rb +79 -0
  15. data/lib/neurohmmerapp/server.rb +63 -0
  16. data/lib/neurohmmerapp/version.rb +3 -0
  17. data/lib/neurohmmerapp.rb +207 -0
  18. data/neurohmmerapp.gemspec +50 -0
  19. data/public/NeuroHmmer/loading.html +12 -0
  20. data/public/src/css/bootstrap1.min.css +7 -0
  21. data/public/src/css/custom.css +189 -0
  22. data/public/src/css/custom.min.css +1 -0
  23. data/public/src/css/font-awesome.min.css +4 -0
  24. data/public/src/js/bionode-seq.min.js +1 -0
  25. data/public/src/js/bootstrap.min.js +6 -0
  26. data/public/src/js/jquery.cookie.min.js +1 -0
  27. data/public/src/js/jquery.min.js +4 -0
  28. data/public/src/js/jquery.validate.min.js +4 -0
  29. data/public/src/js/neurohmmer.js +228 -0
  30. data/public/src/js/neurohmmer.min.js +1 -0
  31. data/public/web_files/css/nh_compiled_css.min.css +14 -0
  32. data/public/web_files/fonts/FontAwesome.otf +0 -0
  33. data/public/web_files/fonts/fontawesome-webfont.eot +0 -0
  34. data/public/web_files/fonts/fontawesome-webfont.svg +504 -0
  35. data/public/web_files/fonts/fontawesome-webfont.ttf +0 -0
  36. data/public/web_files/fonts/fontawesome-webfont.woff +0 -0
  37. data/public/web_files/js/nh_compiled_js.min.js +20 -0
  38. data/spec/empty_config.yml +0 -0
  39. data/spec/route_spec.rb +72 -0
  40. data/views/500.slim +5 -0
  41. data/views/index.slim +38 -0
  42. data/views/layout.slim +74 -0
  43. data/views/results.slim +9 -0
  44. metadata +281 -0
checksums.yaml ADDED
@@ -0,0 +1,7 @@
1
+ ---
2
+ SHA1:
3
+ metadata.gz: 0e0d520f45b1e2ecdc92c07614f43fc73f122eb7
4
+ data.tar.gz: 8c7a52cf4b06e3ab3b91c46cb4ab17ef734a2fe8
5
+ SHA512:
6
+ metadata.gz: 7b655903472ebfb36b6748379c6e5f615ff64dc590e9faa952bf8cb9835e5185b84f71eb3b6d3cfa6cef765e7b6ea9863b2a8975945d09c0bc2d00c6aa748870
7
+ data.tar.gz: c79c5df182399717389aeab2fa88fc47d5b2d327d1f64d5dbf912af3bb1dc034136e437271a79c941e95040c210ec02b315ad98cfdd043d5e87487eb68cf24c9
data/.gitignore ADDED
@@ -0,0 +1,24 @@
1
+ *.gem
2
+ *.rbc
3
+ .bundle
4
+ .config
5
+ .yardoc
6
+ .DS_Store
7
+ Gemfile.lock
8
+ InstalledFiles
9
+ _yardoc
10
+ coverage
11
+ doc/
12
+ lib/bundler/man
13
+ pkg
14
+ rdoc
15
+ spec/reports
16
+ test/tmp
17
+ test/version_tmp
18
+ tmp
19
+ *.bundle
20
+ *.so
21
+ *.o
22
+ *.a
23
+ mkmf.log
24
+ .DS_Store
data/Gemfile ADDED
@@ -0,0 +1,4 @@
1
+ source 'https://rubygems.org'
2
+
3
+ # Specify your gem's dependencies in GeneValidatorApp.gemspec
4
+ gemspec
data/Gemfile.lock ADDED
@@ -0,0 +1,81 @@
1
+ PATH
2
+ remote: .
3
+ specs:
4
+ neurohmmerapp (0.0.1)
5
+ bio (~> 1.4)
6
+ neurohmmer (~> 0.1)
7
+ sinatra (~> 1.4)
8
+ sinatra-cross_origin (~> 0.3)
9
+ slim (~> 3.0)
10
+ slop (~> 3.6)
11
+
12
+ GEM
13
+ remote: https://rubygems.org/
14
+ specs:
15
+ bio (1.5.0)
16
+ bio-hmmer3_report (0.1.0)
17
+ bio-logger (~> 1.0)
18
+ bio-logger (1.0.1)
19
+ log4r (>= 1.1.9)
20
+ capybara (2.5.0)
21
+ mime-types (>= 1.16)
22
+ nokogiri (>= 1.3.3)
23
+ rack (>= 1.0.0)
24
+ rack-test (>= 0.5.4)
25
+ xpath (~> 2.0)
26
+ diff-lcs (1.2.5)
27
+ json (1.8.3)
28
+ log4r (1.1.10)
29
+ mime-types (2.6.2)
30
+ mini_portile (0.6.2)
31
+ neurohmmer (0.1.0)
32
+ bio
33
+ bio-hmmer3_report
34
+ slim (~> 3.0)
35
+ nokogiri (1.6.6.2)
36
+ mini_portile (~> 0.6.0)
37
+ rack (1.6.4)
38
+ rack-protection (1.5.3)
39
+ rack
40
+ rack-test (0.6.3)
41
+ rack (>= 1.0)
42
+ rake (10.4.2)
43
+ rspec (2.99.0)
44
+ rspec-core (~> 2.99.0)
45
+ rspec-expectations (~> 2.99.0)
46
+ rspec-mocks (~> 2.99.0)
47
+ rspec-core (2.99.2)
48
+ rspec-expectations (2.99.2)
49
+ diff-lcs (>= 1.1.3, < 2.0)
50
+ rspec-mocks (2.99.4)
51
+ sinatra (1.4.6)
52
+ rack (~> 1.4)
53
+ rack-protection (~> 1.4)
54
+ tilt (>= 1.3, < 3)
55
+ sinatra-cross_origin (0.3.2)
56
+ slim (3.0.6)
57
+ temple (~> 0.7.3)
58
+ tilt (>= 1.3.3, < 2.1)
59
+ slop (3.6.0)
60
+ temple (0.7.6)
61
+ tilt (2.0.1)
62
+ w3c_validators (1.2)
63
+ json
64
+ nokogiri
65
+ xpath (2.0.0)
66
+ nokogiri (~> 1.3)
67
+
68
+ PLATFORMS
69
+ ruby
70
+
71
+ DEPENDENCIES
72
+ bundler (~> 1.6)
73
+ capybara (~> 2.4, >= 2.4.4)
74
+ neurohmmerapp!
75
+ rack-test (~> 0.6)
76
+ rake (~> 10.3)
77
+ rspec (~> 2.8, >= 2.8.0)
78
+ w3c_validators (~> 1.1)
79
+
80
+ BUNDLED WITH
81
+ 1.10.5