scaffolder-tools 0.1.0
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.
- data/.document +5 -0
- data/.rspec +1 -0
- data/Gemfile +23 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +38 -0
- data/Rakefile +41 -0
- data/VERSION +1 -0
- data/bin/scaffolder +14 -0
- data/features/help.feature +79 -0
- data/features/sequence.feature +157 -0
- data/features/step_definitions/scaffolder-tools.rb +4 -0
- data/features/support/env.rb +15 -0
- data/features/validate.feature +245 -0
- data/lib/scaffolder/binary_helper.rb +30 -0
- data/lib/scaffolder/tool/help.rb +57 -0
- data/lib/scaffolder/tool/sequence.rb +34 -0
- data/lib/scaffolder/tool/validate.rb +51 -0
- data/lib/scaffolder/tool.rb +44 -0
- data/lib/scaffolder/tool_index.rb +50 -0
- data/man/scaffolder-help.1.ronn +23 -0
- data/man/scaffolder-sequence.1.ronn +48 -0
- data/man/scaffolder-validate.1.ronn +28 -0
- data/scaffolder-tools.gemspec +125 -0
- data/spec/scaffolder/binary_helper_spec.rb +71 -0
- data/spec/scaffolder/tool/help_spec.rb +127 -0
- data/spec/scaffolder/tool/sequence_spec.rb +41 -0
- data/spec/scaffolder/tool/validate_spec.rb +167 -0
- data/spec/scaffolder/tool_index_spec.rb +49 -0
- data/spec/scaffolder/tool_spec.rb +147 -0
- data/spec/spec_helper.rb +51 -0
- data/spec/support/exit_code_matcher.rb +26 -0
- metadata +330 -0
    
        metadata
    ADDED
    
    | @@ -0,0 +1,330 @@ | |
| 1 | 
            +
            --- !ruby/object:Gem::Specification 
         | 
| 2 | 
            +
            name: scaffolder-tools
         | 
| 3 | 
            +
            version: !ruby/object:Gem::Version 
         | 
| 4 | 
            +
              hash: 27
         | 
| 5 | 
            +
              prerelease: false
         | 
| 6 | 
            +
              segments: 
         | 
| 7 | 
            +
              - 0
         | 
| 8 | 
            +
              - 1
         | 
| 9 | 
            +
              - 0
         | 
| 10 | 
            +
              version: 0.1.0
         | 
| 11 | 
            +
            platform: ruby
         | 
| 12 | 
            +
            authors: 
         | 
| 13 | 
            +
            - Michael Barton
         | 
| 14 | 
            +
            autorequire: 
         | 
| 15 | 
            +
            bindir: bin
         | 
| 16 | 
            +
            cert_chain: []
         | 
| 17 | 
            +
             | 
| 18 | 
            +
            date: 2011-01-04 00:00:00 -05:00
         | 
| 19 | 
            +
            default_executable: scaffolder
         | 
| 20 | 
            +
            dependencies: 
         | 
| 21 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 22 | 
            +
              requirement: &id001 !ruby/object:Gem::Requirement 
         | 
| 23 | 
            +
                none: false
         | 
| 24 | 
            +
                requirements: 
         | 
| 25 | 
            +
                - - ~>
         | 
| 26 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 27 | 
            +
                    hash: 9
         | 
| 28 | 
            +
                    segments: 
         | 
| 29 | 
            +
                    - 0
         | 
| 30 | 
            +
                    - 1
         | 
| 31 | 
            +
                    version: "0.1"
         | 
| 32 | 
            +
              type: :runtime
         | 
| 33 | 
            +
              name: configliere
         | 
| 34 | 
            +
              prerelease: false
         | 
| 35 | 
            +
              version_requirements: *id001
         | 
| 36 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 37 | 
            +
              requirement: &id002 !ruby/object:Gem::Requirement 
         | 
| 38 | 
            +
                none: false
         | 
| 39 | 
            +
                requirements: 
         | 
| 40 | 
            +
                - - ~>
         | 
| 41 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 42 | 
            +
                    hash: 7
         | 
| 43 | 
            +
                    segments: 
         | 
| 44 | 
            +
                    - 1
         | 
| 45 | 
            +
                    - 4
         | 
| 46 | 
            +
                    version: "1.4"
         | 
| 47 | 
            +
              type: :runtime
         | 
| 48 | 
            +
              name: bio
         | 
| 49 | 
            +
              prerelease: false
         | 
| 50 | 
            +
              version_requirements: *id002
         | 
| 51 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 52 | 
            +
              requirement: &id003 !ruby/object:Gem::Requirement 
         | 
| 53 | 
            +
                none: false
         | 
| 54 | 
            +
                requirements: 
         | 
| 55 | 
            +
                - - ~>
         | 
| 56 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 57 | 
            +
                    hash: 3
         | 
| 58 | 
            +
                    segments: 
         | 
| 59 | 
            +
                    - 0
         | 
| 60 | 
            +
                    - 4
         | 
| 61 | 
            +
                    version: "0.4"
         | 
| 62 | 
            +
              type: :runtime
         | 
| 63 | 
            +
              name: scaffolder
         | 
| 64 | 
            +
              prerelease: false
         | 
| 65 | 
            +
              version_requirements: *id003
         | 
| 66 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 67 | 
            +
              requirement: &id004 !ruby/object:Gem::Requirement 
         | 
| 68 | 
            +
                none: false
         | 
| 69 | 
            +
                requirements: 
         | 
| 70 | 
            +
                - - ~>
         | 
| 71 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 72 | 
            +
                    hash: 5
         | 
| 73 | 
            +
                    segments: 
         | 
| 74 | 
            +
                    - 0
         | 
| 75 | 
            +
                    - 7
         | 
| 76 | 
            +
                    version: "0.7"
         | 
| 77 | 
            +
              type: :runtime
         | 
| 78 | 
            +
              name: ronn
         | 
| 79 | 
            +
              prerelease: false
         | 
| 80 | 
            +
              version_requirements: *id004
         | 
| 81 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 82 | 
            +
              requirement: &id005 !ruby/object:Gem::Requirement 
         | 
| 83 | 
            +
                none: false
         | 
| 84 | 
            +
                requirements: 
         | 
| 85 | 
            +
                - - ~>
         | 
| 86 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 87 | 
            +
                    hash: 15
         | 
| 88 | 
            +
                    segments: 
         | 
| 89 | 
            +
                    - 1
         | 
| 90 | 
            +
                    - 0
         | 
| 91 | 
            +
                    version: "1.0"
         | 
| 92 | 
            +
              type: :development
         | 
| 93 | 
            +
              name: bundler
         | 
| 94 | 
            +
              prerelease: false
         | 
| 95 | 
            +
              version_requirements: *id005
         | 
| 96 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 97 | 
            +
              requirement: &id006 !ruby/object:Gem::Requirement 
         | 
| 98 | 
            +
                none: false
         | 
| 99 | 
            +
                requirements: 
         | 
| 100 | 
            +
                - - ~>
         | 
| 101 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 102 | 
            +
                    hash: 5
         | 
| 103 | 
            +
                    segments: 
         | 
| 104 | 
            +
                    - 1
         | 
| 105 | 
            +
                    - 5
         | 
| 106 | 
            +
                    version: "1.5"
         | 
| 107 | 
            +
              type: :development
         | 
| 108 | 
            +
              name: jeweler
         | 
| 109 | 
            +
              prerelease: false
         | 
| 110 | 
            +
              version_requirements: *id006
         | 
| 111 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 112 | 
            +
              requirement: &id007 !ruby/object:Gem::Requirement 
         | 
| 113 | 
            +
                none: false
         | 
| 114 | 
            +
                requirements: 
         | 
| 115 | 
            +
                - - ~>
         | 
| 116 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 117 | 
            +
                    hash: 5
         | 
| 118 | 
            +
                    segments: 
         | 
| 119 | 
            +
                    - 2
         | 
| 120 | 
            +
                    - 3
         | 
| 121 | 
            +
                    - 3
         | 
| 122 | 
            +
                    version: 2.3.3
         | 
| 123 | 
            +
              type: :development
         | 
| 124 | 
            +
              name: gherkin
         | 
| 125 | 
            +
              prerelease: false
         | 
| 126 | 
            +
              version_requirements: *id007
         | 
| 127 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 128 | 
            +
              requirement: &id008 !ruby/object:Gem::Requirement 
         | 
| 129 | 
            +
                none: false
         | 
| 130 | 
            +
                requirements: 
         | 
| 131 | 
            +
                - - ~>
         | 
| 132 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 133 | 
            +
                    hash: 11
         | 
| 134 | 
            +
                    segments: 
         | 
| 135 | 
            +
                    - 2
         | 
| 136 | 
            +
                    - 4
         | 
| 137 | 
            +
                    version: "2.4"
         | 
| 138 | 
            +
              type: :development
         | 
| 139 | 
            +
              name: rspec
         | 
| 140 | 
            +
              prerelease: false
         | 
| 141 | 
            +
              version_requirements: *id008
         | 
| 142 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 143 | 
            +
              requirement: &id009 !ruby/object:Gem::Requirement 
         | 
| 144 | 
            +
                none: false
         | 
| 145 | 
            +
                requirements: 
         | 
| 146 | 
            +
                - - ~>
         | 
| 147 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 148 | 
            +
                    hash: 31
         | 
| 149 | 
            +
                    segments: 
         | 
| 150 | 
            +
                    - 0
         | 
| 151 | 
            +
                    - 10
         | 
| 152 | 
            +
                    version: "0.10"
         | 
| 153 | 
            +
              type: :development
         | 
| 154 | 
            +
              name: cucumber
         | 
| 155 | 
            +
              prerelease: false
         | 
| 156 | 
            +
              version_requirements: *id009
         | 
| 157 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 158 | 
            +
              requirement: &id010 !ruby/object:Gem::Requirement 
         | 
| 159 | 
            +
                none: false
         | 
| 160 | 
            +
                requirements: 
         | 
| 161 | 
            +
                - - ~>
         | 
| 162 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 163 | 
            +
                    hash: 15
         | 
| 164 | 
            +
                    segments: 
         | 
| 165 | 
            +
                    - 0
         | 
| 166 | 
            +
                    - 2
         | 
| 167 | 
            +
                    version: "0.2"
         | 
| 168 | 
            +
              type: :development
         | 
| 169 | 
            +
              name: fakefs
         | 
| 170 | 
            +
              prerelease: false
         | 
| 171 | 
            +
              version_requirements: *id010
         | 
| 172 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 173 | 
            +
              requirement: &id011 !ruby/object:Gem::Requirement 
         | 
| 174 | 
            +
                none: false
         | 
| 175 | 
            +
                requirements: 
         | 
| 176 | 
            +
                - - ~>
         | 
| 177 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 178 | 
            +
                    hash: 15
         | 
| 179 | 
            +
                    segments: 
         | 
| 180 | 
            +
                    - 0
         | 
| 181 | 
            +
                    - 2
         | 
| 182 | 
            +
                    version: "0.2"
         | 
| 183 | 
            +
              type: :development
         | 
| 184 | 
            +
              name: aruba
         | 
| 185 | 
            +
              prerelease: false
         | 
| 186 | 
            +
              version_requirements: *id011
         | 
| 187 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 188 | 
            +
              requirement: &id012 !ruby/object:Gem::Requirement 
         | 
| 189 | 
            +
                none: false
         | 
| 190 | 
            +
                requirements: 
         | 
| 191 | 
            +
                - - ~>
         | 
| 192 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 193 | 
            +
                    hash: 25
         | 
| 194 | 
            +
                    segments: 
         | 
| 195 | 
            +
                    - 0
         | 
| 196 | 
            +
                    - 9
         | 
| 197 | 
            +
                    version: "0.9"
         | 
| 198 | 
            +
              type: :development
         | 
| 199 | 
            +
              name: mocha
         | 
| 200 | 
            +
              prerelease: false
         | 
| 201 | 
            +
              version_requirements: *id012
         | 
| 202 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 203 | 
            +
              requirement: &id013 !ruby/object:Gem::Requirement 
         | 
| 204 | 
            +
                none: false
         | 
| 205 | 
            +
                requirements: 
         | 
| 206 | 
            +
                - - ~>
         | 
| 207 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 208 | 
            +
                    hash: 3
         | 
| 209 | 
            +
                    segments: 
         | 
| 210 | 
            +
                    - 0
         | 
| 211 | 
            +
                    - 4
         | 
| 212 | 
            +
                    version: "0.4"
         | 
| 213 | 
            +
              type: :development
         | 
| 214 | 
            +
              name: hashie
         | 
| 215 | 
            +
              prerelease: false
         | 
| 216 | 
            +
              version_requirements: *id013
         | 
| 217 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 218 | 
            +
              requirement: &id014 !ruby/object:Gem::Requirement 
         | 
| 219 | 
            +
                none: false
         | 
| 220 | 
            +
                requirements: 
         | 
| 221 | 
            +
                - - ~>
         | 
| 222 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 223 | 
            +
                    hash: 7
         | 
| 224 | 
            +
                    segments: 
         | 
| 225 | 
            +
                    - 0
         | 
| 226 | 
            +
                    - 6
         | 
| 227 | 
            +
                    version: "0.6"
         | 
| 228 | 
            +
              type: :development
         | 
| 229 | 
            +
              name: yard
         | 
| 230 | 
            +
              prerelease: false
         | 
| 231 | 
            +
              version_requirements: *id014
         | 
| 232 | 
            +
            - !ruby/object:Gem::Dependency 
         | 
| 233 | 
            +
              requirement: &id015 !ruby/object:Gem::Requirement 
         | 
| 234 | 
            +
                none: false
         | 
| 235 | 
            +
                requirements: 
         | 
| 236 | 
            +
                - - ~>
         | 
| 237 | 
            +
                  - !ruby/object:Gem::Version 
         | 
| 238 | 
            +
                    hash: 9
         | 
| 239 | 
            +
                    segments: 
         | 
| 240 | 
            +
                    - 0
         | 
| 241 | 
            +
                    - 1
         | 
| 242 | 
            +
                    version: "0.1"
         | 
| 243 | 
            +
              type: :development
         | 
| 244 | 
            +
              name: scaffolder-test-helpers
         | 
| 245 | 
            +
              prerelease: false
         | 
| 246 | 
            +
              version_requirements: *id015
         | 
| 247 | 
            +
            description: Binary to use with scaffolder genome scaffolds
         | 
| 248 | 
            +
            email: mail@michaelbarton.me.uk
         | 
| 249 | 
            +
            executables: 
         | 
| 250 | 
            +
            - scaffolder
         | 
| 251 | 
            +
            extensions: []
         | 
| 252 | 
            +
             | 
| 253 | 
            +
            extra_rdoc_files: 
         | 
| 254 | 
            +
            - LICENSE.txt
         | 
| 255 | 
            +
            - README.rdoc
         | 
| 256 | 
            +
            files: 
         | 
| 257 | 
            +
            - .document
         | 
| 258 | 
            +
            - .rspec
         | 
| 259 | 
            +
            - Gemfile
         | 
| 260 | 
            +
            - LICENSE.txt
         | 
| 261 | 
            +
            - README.rdoc
         | 
| 262 | 
            +
            - Rakefile
         | 
| 263 | 
            +
            - VERSION
         | 
| 264 | 
            +
            - bin/scaffolder
         | 
| 265 | 
            +
            - features/help.feature
         | 
| 266 | 
            +
            - features/sequence.feature
         | 
| 267 | 
            +
            - features/step_definitions/scaffolder-tools.rb
         | 
| 268 | 
            +
            - features/support/env.rb
         | 
| 269 | 
            +
            - features/validate.feature
         | 
| 270 | 
            +
            - lib/scaffolder/binary_helper.rb
         | 
| 271 | 
            +
            - lib/scaffolder/tool.rb
         | 
| 272 | 
            +
            - lib/scaffolder/tool/help.rb
         | 
| 273 | 
            +
            - lib/scaffolder/tool/sequence.rb
         | 
| 274 | 
            +
            - lib/scaffolder/tool/validate.rb
         | 
| 275 | 
            +
            - lib/scaffolder/tool_index.rb
         | 
| 276 | 
            +
            - man/scaffolder-help.1.ronn
         | 
| 277 | 
            +
            - man/scaffolder-sequence.1.ronn
         | 
| 278 | 
            +
            - man/scaffolder-validate.1.ronn
         | 
| 279 | 
            +
            - scaffolder-tools.gemspec
         | 
| 280 | 
            +
            - spec/scaffolder/binary_helper_spec.rb
         | 
| 281 | 
            +
            - spec/scaffolder/tool/help_spec.rb
         | 
| 282 | 
            +
            - spec/scaffolder/tool/sequence_spec.rb
         | 
| 283 | 
            +
            - spec/scaffolder/tool/validate_spec.rb
         | 
| 284 | 
            +
            - spec/scaffolder/tool_index_spec.rb
         | 
| 285 | 
            +
            - spec/scaffolder/tool_spec.rb
         | 
| 286 | 
            +
            - spec/spec_helper.rb
         | 
| 287 | 
            +
            - spec/support/exit_code_matcher.rb
         | 
| 288 | 
            +
            has_rdoc: true
         | 
| 289 | 
            +
            homepage: http://github.com/michaelbarton/scaffolder-tools
         | 
| 290 | 
            +
            licenses: 
         | 
| 291 | 
            +
            - MIT
         | 
| 292 | 
            +
            post_install_message: 
         | 
| 293 | 
            +
            rdoc_options: []
         | 
| 294 | 
            +
             | 
| 295 | 
            +
            require_paths: 
         | 
| 296 | 
            +
            - lib
         | 
| 297 | 
            +
            required_ruby_version: !ruby/object:Gem::Requirement 
         | 
| 298 | 
            +
              none: false
         | 
| 299 | 
            +
              requirements: 
         | 
| 300 | 
            +
              - - ">="
         | 
| 301 | 
            +
                - !ruby/object:Gem::Version 
         | 
| 302 | 
            +
                  hash: 3
         | 
| 303 | 
            +
                  segments: 
         | 
| 304 | 
            +
                  - 0
         | 
| 305 | 
            +
                  version: "0"
         | 
| 306 | 
            +
            required_rubygems_version: !ruby/object:Gem::Requirement 
         | 
| 307 | 
            +
              none: false
         | 
| 308 | 
            +
              requirements: 
         | 
| 309 | 
            +
              - - ">="
         | 
| 310 | 
            +
                - !ruby/object:Gem::Version 
         | 
| 311 | 
            +
                  hash: 3
         | 
| 312 | 
            +
                  segments: 
         | 
| 313 | 
            +
                  - 0
         | 
| 314 | 
            +
                  version: "0"
         | 
| 315 | 
            +
            requirements: []
         | 
| 316 | 
            +
             | 
| 317 | 
            +
            rubyforge_project: 
         | 
| 318 | 
            +
            rubygems_version: 1.3.7
         | 
| 319 | 
            +
            signing_key: 
         | 
| 320 | 
            +
            specification_version: 3
         | 
| 321 | 
            +
            summary: Tools for manipulating genome scaffolds
         | 
| 322 | 
            +
            test_files: 
         | 
| 323 | 
            +
            - spec/scaffolder/binary_helper_spec.rb
         | 
| 324 | 
            +
            - spec/scaffolder/tool/help_spec.rb
         | 
| 325 | 
            +
            - spec/scaffolder/tool/sequence_spec.rb
         | 
| 326 | 
            +
            - spec/scaffolder/tool/validate_spec.rb
         | 
| 327 | 
            +
            - spec/scaffolder/tool_index_spec.rb
         | 
| 328 | 
            +
            - spec/scaffolder/tool_spec.rb
         | 
| 329 | 
            +
            - spec/spec_helper.rb
         | 
| 330 | 
            +
            - spec/support/exit_code_matcher.rb
         |