miga-base 0.2.0.6

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Files changed (52) hide show
  1. checksums.yaml +7 -0
  2. data/README.md +351 -0
  3. data/actions/add_result +61 -0
  4. data/actions/add_taxonomy +86 -0
  5. data/actions/create_dataset +62 -0
  6. data/actions/create_project +70 -0
  7. data/actions/daemon +69 -0
  8. data/actions/download_dataset +77 -0
  9. data/actions/find_datasets +63 -0
  10. data/actions/import_datasets +86 -0
  11. data/actions/index_taxonomy +71 -0
  12. data/actions/list_datasets +83 -0
  13. data/actions/list_files +67 -0
  14. data/actions/unlink_dataset +52 -0
  15. data/bin/miga +48 -0
  16. data/lib/miga/daemon.rb +178 -0
  17. data/lib/miga/dataset.rb +286 -0
  18. data/lib/miga/gui.rb +289 -0
  19. data/lib/miga/metadata.rb +74 -0
  20. data/lib/miga/project.rb +268 -0
  21. data/lib/miga/remote_dataset.rb +154 -0
  22. data/lib/miga/result.rb +102 -0
  23. data/lib/miga/tax_index.rb +70 -0
  24. data/lib/miga/taxonomy.rb +107 -0
  25. data/lib/miga.rb +83 -0
  26. data/scripts/_distances_noref_nomulti.bash +86 -0
  27. data/scripts/_distances_ref_nomulti.bash +105 -0
  28. data/scripts/aai_distances.bash +40 -0
  29. data/scripts/ani_distances.bash +39 -0
  30. data/scripts/assembly.bash +38 -0
  31. data/scripts/cds.bash +45 -0
  32. data/scripts/clade_finding.bash +27 -0
  33. data/scripts/distances.bash +30 -0
  34. data/scripts/essential_genes.bash +29 -0
  35. data/scripts/haai_distances.bash +39 -0
  36. data/scripts/init.bash +211 -0
  37. data/scripts/miga.bash +12 -0
  38. data/scripts/mytaxa.bash +93 -0
  39. data/scripts/mytaxa_scan.bash +85 -0
  40. data/scripts/ogs.bash +36 -0
  41. data/scripts/read_quality.bash +37 -0
  42. data/scripts/ssu.bash +35 -0
  43. data/scripts/subclades.bash +26 -0
  44. data/scripts/trimmed_fasta.bash +47 -0
  45. data/scripts/trimmed_reads.bash +57 -0
  46. data/utils/adapters.fa +302 -0
  47. data/utils/mytaxa_scan.R +89 -0
  48. data/utils/mytaxa_scan.rb +58 -0
  49. data/utils/requirements.txt +19 -0
  50. data/utils/subclades-compile.rb +48 -0
  51. data/utils/subclades.R +171 -0
  52. metadata +185 -0
metadata ADDED
@@ -0,0 +1,185 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: miga-base
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.2.0.6
5
+ platform: ruby
6
+ authors:
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+ - Luis M. Rodriguez-R
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+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2015-12-07 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
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+ name: rest-client
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+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - ~>
18
+ - !ruby/object:Gem::Version
19
+ version: '1.7'
20
+ type: :runtime
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - ~>
25
+ - !ruby/object:Gem::Version
26
+ version: '1.7'
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+ - !ruby/object:Gem::Dependency
28
+ name: sqlite3
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ~>
32
+ - !ruby/object:Gem::Version
33
+ version: '1.3'
34
+ type: :runtime
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - ~>
39
+ - !ruby/object:Gem::Version
40
+ version: '1.3'
41
+ - !ruby/object:Gem::Dependency
42
+ name: daemons
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ~>
46
+ - !ruby/object:Gem::Version
47
+ version: '1.2'
48
+ type: :runtime
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ~>
53
+ - !ruby/object:Gem::Version
54
+ version: '1.2'
55
+ - !ruby/object:Gem::Dependency
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+ name: json
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
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+ version: '1.8'
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+ type: :runtime
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
66
+ - - ~>
67
+ - !ruby/object:Gem::Version
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+ version: '1.8'
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+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
73
+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
77
+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
80
+ - - '>='
81
+ - !ruby/object:Gem::Version
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+ version: '0'
83
+ - !ruby/object:Gem::Dependency
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+ name: test-unit
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
87
+ - - '>='
88
+ - !ruby/object:Gem::Version
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+ version: '0'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
94
+ - - '>='
95
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ description: Microbial Genomes Atlas
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+ email: lmrodriguezr@gmail.com
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+ executables:
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+ - miga
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+ extensions: []
102
+ extra_rdoc_files:
103
+ - README.md
104
+ files:
105
+ - lib/miga.rb
106
+ - lib/miga/daemon.rb
107
+ - lib/miga/dataset.rb
108
+ - lib/miga/gui.rb
109
+ - lib/miga/metadata.rb
110
+ - lib/miga/project.rb
111
+ - lib/miga/remote_dataset.rb
112
+ - lib/miga/result.rb
113
+ - lib/miga/tax_index.rb
114
+ - lib/miga/taxonomy.rb
115
+ - scripts/_distances_noref_nomulti.bash
116
+ - scripts/_distances_ref_nomulti.bash
117
+ - scripts/aai_distances.bash
118
+ - scripts/ani_distances.bash
119
+ - scripts/assembly.bash
120
+ - scripts/cds.bash
121
+ - scripts/clade_finding.bash
122
+ - scripts/distances.bash
123
+ - scripts/essential_genes.bash
124
+ - scripts/haai_distances.bash
125
+ - scripts/init.bash
126
+ - scripts/miga.bash
127
+ - scripts/mytaxa.bash
128
+ - scripts/mytaxa_scan.bash
129
+ - scripts/ogs.bash
130
+ - scripts/read_quality.bash
131
+ - scripts/ssu.bash
132
+ - scripts/subclades.bash
133
+ - scripts/trimmed_fasta.bash
134
+ - scripts/trimmed_reads.bash
135
+ - utils/adapters.fa
136
+ - utils/mytaxa_scan.R
137
+ - utils/mytaxa_scan.rb
138
+ - utils/requirements.txt
139
+ - utils/subclades-compile.rb
140
+ - utils/subclades.R
141
+ - bin/miga
142
+ - actions/add_result
143
+ - actions/add_taxonomy
144
+ - actions/create_dataset
145
+ - actions/create_project
146
+ - actions/daemon
147
+ - actions/download_dataset
148
+ - actions/find_datasets
149
+ - actions/import_datasets
150
+ - actions/index_taxonomy
151
+ - actions/list_datasets
152
+ - actions/list_files
153
+ - actions/unlink_dataset
154
+ - README.md
155
+ homepage: http://enve-omics.ce.gatech.edu/miga
156
+ licenses:
157
+ - artistic 2.0
158
+ metadata: {}
159
+ post_install_message:
160
+ rdoc_options:
161
+ - lib
162
+ - README.md
163
+ - --main
164
+ - README.md
165
+ - --title
166
+ - MiGA
167
+ require_paths:
168
+ - lib
169
+ required_ruby_version: !ruby/object:Gem::Requirement
170
+ requirements:
171
+ - - ~>
172
+ - !ruby/object:Gem::Version
173
+ version: '2.0'
174
+ required_rubygems_version: !ruby/object:Gem::Requirement
175
+ requirements:
176
+ - - '>='
177
+ - !ruby/object:Gem::Version
178
+ version: '0'
179
+ requirements: []
180
+ rubyforge_project:
181
+ rubygems_version: 2.0.14
182
+ signing_key:
183
+ specification_version: 4
184
+ summary: MiGA
185
+ test_files: []