scaffolder-annotation-locator 0.1.0 → 0.1.1

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.
Files changed (5) hide show
  1. data/Gemfile +3 -1
  2. data/Rakefile +2 -1
  3. data/VERSION +1 -1
  4. data/scaffolder-annotation-locator.gemspec +17 -12
  5. metadata +106 -132
data/Gemfile CHANGED
@@ -1,7 +1,9 @@
1
1
  source "http://rubygems.org"
2
2
 
3
3
  group :default do
4
- gem "scaffolder", "0.4.3"
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+ gem "scaffolder", ">= 0.4.3"
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+ gem "bio", "~> 1.4"
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+ gem "psych"
5
7
  end
6
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  group :development do
data/Rakefile CHANGED
@@ -7,6 +7,7 @@ rescue Bundler::BundlerError => e
7
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  $stderr.puts "Run `bundle install` to install missing gems"
8
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  exit e.status_code
9
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  end
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+ require 'rake/dsl_definition'
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  require 'rake'
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12
 
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  require 'jeweler'
@@ -17,7 +18,7 @@ Jeweler::Tasks.new do |gem|
17
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  gem.license = "MIT"
18
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  gem.summary = %Q{Update locations of gff3 annotations from a scaffolder template}
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  gem.description = %Q{Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffolder tempalte as a base.}
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- gem.email = "mail@michaelbarton.me.uk"
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+ gem.email = "mail@next.gs"
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  gem.authors = ["Michael Barton"]
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  end
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  Jeweler::RubygemsDotOrgTasks.new
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.1.0
1
+ 0.1.1
data/scaffolder-annotation-locator.gemspec CHANGED
@@ -4,14 +4,14 @@
4
4
  # -*- encoding: utf-8 -*-
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5
 
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  Gem::Specification.new do |s|
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- s.name = %q{scaffolder-annotation-locator}
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- s.version = "0.1.0"
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+ s.name = "scaffolder-annotation-locator"
8
+ s.version = "0.1.1"
9
9
 
10
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
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  s.authors = ["Michael Barton"]
12
- s.date = %q{2011-06-10}
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- s.description = %q{Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffolder tempalte as a base.}
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- s.email = %q{mail@michaelbarton.me.uk}
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+ s.date = "2012-01-26"
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+ s.description = "Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffolder tempalte as a base."
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+ s.email = "mail@next.gs"
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  s.extra_rdoc_files = [
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  "LICENSE.txt",
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  "README.rdoc"
@@ -38,18 +38,19 @@ Gem::Specification.new do |s|
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  "spec/spec_helper.rb",
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  "spec/support/gff_attribute_matcher.rb"
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  ]
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- s.homepage = %q{http://next.gs}
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+ s.homepage = "http://next.gs"
42
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  s.licenses = ["MIT"]
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  s.require_paths = ["lib"]
44
- s.rubygems_version = %q{1.3.7}
45
- s.summary = %q{Update locations of gff3 annotations from a scaffolder template}
44
+ s.rubygems_version = "1.8.11"
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+ s.summary = "Update locations of gff3 annotations from a scaffolder template"
46
46
 
47
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  if s.respond_to? :specification_version then
48
- current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
49
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  s.specification_version = 3
50
49
 
51
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  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
52
- s.add_runtime_dependency(%q<scaffolder>, ["= 0.4.3"])
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+ s.add_runtime_dependency(%q<scaffolder>, [">= 0.4.3"])
52
+ s.add_runtime_dependency(%q<bio>, ["~> 1.4"])
53
+ s.add_runtime_dependency(%q<psych>, [">= 0"])
53
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  s.add_development_dependency(%q<bundler>, ["~> 1.0"])
54
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  s.add_development_dependency(%q<jeweler>, ["~> 1.5"])
55
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  s.add_development_dependency(%q<rspec>, ["~> 2.4"])
@@ -58,7 +59,9 @@ Gem::Specification.new do |s|
58
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  s.add_development_dependency(%q<aruba>, ["~> 0.2"])
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  s.add_development_dependency(%q<yard>, ["~> 0.6"])
60
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  else
61
- s.add_dependency(%q<scaffolder>, ["= 0.4.3"])
62
+ s.add_dependency(%q<scaffolder>, [">= 0.4.3"])
63
+ s.add_dependency(%q<bio>, ["~> 1.4"])
64
+ s.add_dependency(%q<psych>, [">= 0"])
62
65
  s.add_dependency(%q<bundler>, ["~> 1.0"])
63
66
  s.add_dependency(%q<jeweler>, ["~> 1.5"])
64
67
  s.add_dependency(%q<rspec>, ["~> 2.4"])
@@ -68,7 +71,9 @@ Gem::Specification.new do |s|
68
71
  s.add_dependency(%q<yard>, ["~> 0.6"])
69
72
  end
70
73
  else
71
- s.add_dependency(%q<scaffolder>, ["= 0.4.3"])
74
+ s.add_dependency(%q<scaffolder>, [">= 0.4.3"])
75
+ s.add_dependency(%q<bio>, ["~> 1.4"])
76
+ s.add_dependency(%q<psych>, [">= 0"])
72
77
  s.add_dependency(%q<bundler>, ["~> 1.0"])
73
78
  s.add_dependency(%q<jeweler>, ["~> 1.5"])
74
79
  s.add_dependency(%q<rspec>, ["~> 2.4"])
metadata CHANGED
@@ -1,155 +1,136 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: scaffolder-annotation-locator
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
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.1
5
+ prerelease:
11
6
  platform: ruby
12
- authors:
7
+ authors:
13
8
  - Michael Barton
14
9
  autorequire:
15
10
  bindir: bin
16
11
  cert_chain: []
17
-
18
- date: 2011-06-10 00:00:00 -04:00
19
- default_executable:
20
- dependencies:
21
- - !ruby/object:Gem::Dependency
22
- requirement: &id001 !ruby/object:Gem::Requirement
12
+ date: 2012-01-26 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: scaffolder
16
+ requirement: &70157864359580 !ruby/object:Gem::Requirement
23
17
  none: false
24
- requirements:
25
- - - "="
26
- - !ruby/object:Gem::Version
27
- hash: 9
28
- segments:
29
- - 0
30
- - 4
31
- - 3
18
+ requirements:
19
+ - - ! '>='
20
+ - !ruby/object:Gem::Version
32
21
  version: 0.4.3
33
22
  type: :runtime
34
- name: scaffolder
35
23
  prerelease: false
36
- version_requirements: *id001
37
- - !ruby/object:Gem::Dependency
38
- requirement: &id002 !ruby/object:Gem::Requirement
24
+ version_requirements: *70157864359580
25
+ - !ruby/object:Gem::Dependency
26
+ name: bio
27
+ requirement: &70157864356600 !ruby/object:Gem::Requirement
39
28
  none: false
40
- requirements:
29
+ requirements:
41
30
  - - ~>
42
- - !ruby/object:Gem::Version
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- hash: 15
44
- segments:
45
- - 1
46
- - 0
47
- version: "1.0"
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- type: :development
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- name: bundler
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+ - !ruby/object:Gem::Version
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+ version: '1.4'
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+ type: :runtime
50
34
  prerelease: false
51
- version_requirements: *id002
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- - !ruby/object:Gem::Dependency
53
- requirement: &id003 !ruby/object:Gem::Requirement
35
+ version_requirements: *70157864356600
36
+ - !ruby/object:Gem::Dependency
37
+ name: psych
38
+ requirement: &70157864369780 !ruby/object:Gem::Requirement
54
39
  none: false
55
- requirements:
40
+ requirements:
41
+ - - ! '>='
42
+ - !ruby/object:Gem::Version
43
+ version: '0'
44
+ type: :runtime
45
+ prerelease: false
46
+ version_requirements: *70157864369780
47
+ - !ruby/object:Gem::Dependency
48
+ name: bundler
49
+ requirement: &70157864365900 !ruby/object:Gem::Requirement
50
+ none: false
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+ requirements:
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52
  - - ~>
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- - !ruby/object:Gem::Version
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- hash: 5
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- segments:
60
- - 1
61
- - 5
62
- version: "1.5"
53
+ - !ruby/object:Gem::Version
54
+ version: '1.0'
63
55
  type: :development
64
- name: jeweler
65
56
  prerelease: false
66
- version_requirements: *id003
67
- - !ruby/object:Gem::Dependency
68
- requirement: &id004 !ruby/object:Gem::Requirement
57
+ version_requirements: *70157864365900
58
+ - !ruby/object:Gem::Dependency
59
+ name: jeweler
60
+ requirement: &70157864379040 !ruby/object:Gem::Requirement
69
61
  none: false
70
- requirements:
62
+ requirements:
71
63
  - - ~>
72
- - !ruby/object:Gem::Version
73
- hash: 11
74
- segments:
75
- - 2
76
- - 4
77
- version: "2.4"
64
+ - !ruby/object:Gem::Version
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+ version: '1.5'
78
66
  type: :development
67
+ prerelease: false
68
+ version_requirements: *70157864379040
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+ - !ruby/object:Gem::Dependency
79
70
  name: rspec
71
+ requirement: &70157864375160 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
74
+ - - ~>
75
+ - !ruby/object:Gem::Version
76
+ version: '2.4'
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+ type: :development
80
78
  prerelease: false
81
- version_requirements: *id004
82
- - !ruby/object:Gem::Dependency
83
- requirement: &id005 !ruby/object:Gem::Requirement
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+ version_requirements: *70157864375160
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+ - !ruby/object:Gem::Dependency
81
+ name: scaffolder-test-helpers
82
+ requirement: &70157864371800 !ruby/object:Gem::Requirement
84
83
  none: false
85
- requirements:
86
- - - "="
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- - !ruby/object:Gem::Version
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- hash: 19
89
- segments:
90
- - 0
91
- - 3
92
- - 0
84
+ requirements:
85
+ - - =
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+ - !ruby/object:Gem::Version
93
87
  version: 0.3.0
94
88
  type: :development
95
- name: scaffolder-test-helpers
96
89
  prerelease: false
97
- version_requirements: *id005
98
- - !ruby/object:Gem::Dependency
99
- requirement: &id006 !ruby/object:Gem::Requirement
90
+ version_requirements: *70157864371800
91
+ - !ruby/object:Gem::Dependency
92
+ name: cucumber
93
+ requirement: &70157871937940 !ruby/object:Gem::Requirement
100
94
  none: false
101
- requirements:
95
+ requirements:
102
96
  - - ~>
103
- - !ruby/object:Gem::Version
104
- hash: 25
105
- segments:
106
- - 0
107
- - 9
108
- version: "0.9"
97
+ - !ruby/object:Gem::Version
98
+ version: '0.9'
109
99
  type: :development
110
- name: cucumber
111
100
  prerelease: false
112
- version_requirements: *id006
113
- - !ruby/object:Gem::Dependency
114
- requirement: &id007 !ruby/object:Gem::Requirement
101
+ version_requirements: *70157871937940
102
+ - !ruby/object:Gem::Dependency
103
+ name: aruba
104
+ requirement: &70157871936900 !ruby/object:Gem::Requirement
115
105
  none: false
116
- requirements:
106
+ requirements:
117
107
  - - ~>
118
- - !ruby/object:Gem::Version
119
- hash: 15
120
- segments:
121
- - 0
122
- - 2
123
- version: "0.2"
108
+ - !ruby/object:Gem::Version
109
+ version: '0.2'
124
110
  type: :development
125
- name: aruba
126
111
  prerelease: false
127
- version_requirements: *id007
128
- - !ruby/object:Gem::Dependency
129
- requirement: &id008 !ruby/object:Gem::Requirement
112
+ version_requirements: *70157871936900
113
+ - !ruby/object:Gem::Dependency
114
+ name: yard
115
+ requirement: &70157871935380 !ruby/object:Gem::Requirement
130
116
  none: false
131
- requirements:
117
+ requirements:
132
118
  - - ~>
133
- - !ruby/object:Gem::Version
134
- hash: 7
135
- segments:
136
- - 0
137
- - 6
138
- version: "0.6"
119
+ - !ruby/object:Gem::Version
120
+ version: '0.6'
139
121
  type: :development
140
- name: yard
141
122
  prerelease: false
142
- version_requirements: *id008
143
- description: Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffolder tempalte as a base.
144
- email: mail@michaelbarton.me.uk
123
+ version_requirements: *70157871935380
124
+ description: Build a genome scaffold using scaffolder and a set of annotated contigs.
125
+ This tool updates the locations of the contig annotations using the scaffolder tempalte
126
+ as a base.
127
+ email: mail@next.gs
145
128
  executables: []
146
-
147
129
  extensions: []
148
-
149
- extra_rdoc_files:
130
+ extra_rdoc_files:
150
131
  - LICENSE.txt
151
132
  - README.rdoc
152
- files:
133
+ files:
153
134
  - .document
154
135
  - Gemfile
155
136
  - LICENSE.txt
@@ -170,39 +151,32 @@ files:
170
151
  - spec/scaffolder/gff_record_helper_spec.rb
171
152
  - spec/spec_helper.rb
172
153
  - spec/support/gff_attribute_matcher.rb
173
- has_rdoc: true
174
154
  homepage: http://next.gs
175
- licenses:
155
+ licenses:
176
156
  - MIT
177
157
  post_install_message:
178
158
  rdoc_options: []
179
-
180
- require_paths:
159
+ require_paths:
181
160
  - lib
182
- required_ruby_version: !ruby/object:Gem::Requirement
161
+ required_ruby_version: !ruby/object:Gem::Requirement
183
162
  none: false
184
- requirements:
185
- - - ">="
186
- - !ruby/object:Gem::Version
187
- hash: 3
188
- segments:
163
+ requirements:
164
+ - - ! '>='
165
+ - !ruby/object:Gem::Version
166
+ version: '0'
167
+ segments:
189
168
  - 0
190
- version: "0"
191
- required_rubygems_version: !ruby/object:Gem::Requirement
169
+ hash: -1068640633611636753
170
+ required_rubygems_version: !ruby/object:Gem::Requirement
192
171
  none: false
193
- requirements:
194
- - - ">="
195
- - !ruby/object:Gem::Version
196
- hash: 3
197
- segments:
198
- - 0
199
- version: "0"
172
+ requirements:
173
+ - - ! '>='
174
+ - !ruby/object:Gem::Version
175
+ version: '0'
200
176
  requirements: []
201
-
202
177
  rubyforge_project:
203
- rubygems_version: 1.3.7
178
+ rubygems_version: 1.8.11
204
179
  signing_key:
205
180
  specification_version: 3
206
181
  summary: Update locations of gff3 annotations from a scaffolder template
207
182
  test_files: []
208
-