scaffolder-annotation-locator 0.1.0 → 0.1.1

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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
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  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
8
 
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  group :development do
data/Rakefile CHANGED
@@ -7,6 +7,7 @@ rescue Bundler::BundlerError => e
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  $stderr.puts "Run `bundle install` to install missing gems"
8
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  exit e.status_code
9
9
  end
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+ require 'rake/dsl_definition'
10
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  require 'rake'
11
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}
19
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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"
7
+ s.name = "scaffolder-annotation-locator"
8
+ s.version = "0.1.1"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
11
  s.authors = ["Michael Barton"]
12
- s.date = %q{2011-06-10}
13
- 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."
14
+ 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"
40
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  ]
41
- s.homepage = %q{http://next.gs}
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+ s.homepage = "http://next.gs"
42
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  s.licenses = ["MIT"]
43
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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"
45
+ s.summary = "Update locations of gff3 annotations from a scaffolder template"
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46
 
47
47
  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
50
  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
52
- s.add_runtime_dependency(%q<scaffolder>, ["= 0.4.3"])
51
+ 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"])
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54
  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|
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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
61
  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"
48
- type: :development
49
- name: bundler
31
+ - !ruby/object:Gem::Version
32
+ version: '1.4'
33
+ type: :runtime
50
34
  prerelease: false
51
- version_requirements: *id002
52
- - !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
51
+ requirements:
56
52
  - - ~>
57
- - !ruby/object:Gem::Version
58
- hash: 5
59
- segments:
60
- - 1
61
- - 5
62
- version: "1.5"
53
+ - !ruby/object:Gem::Version
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+ 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
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  none: false
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- requirements:
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+ requirements:
71
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  - - ~>
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- - !ruby/object:Gem::Version
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- hash: 11
74
- segments:
75
- - 2
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- - 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
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+ requirement: &70157864375160 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
74
+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '2.4'
77
+ type: :development
80
78
  prerelease: false
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- version_requirements: *id004
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- - !ruby/object:Gem::Dependency
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- 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
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  none: false
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- requirements:
86
- - - "="
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- - !ruby/object:Gem::Version
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- hash: 19
89
- segments:
90
- - 0
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- - 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:
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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
-