scaffolder-tools 0.1.2 → 0.1.3

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.
@@ -1,4 +1,4 @@
1
- require File.expand_path(File.join(File.dirname(__FILE__),'..','..','spec_helper'))
1
+ require 'spec_helper'
2
2
 
3
3
  describe Scaffolder::Tool::Sequence do
4
4
 
@@ -11,29 +11,68 @@ describe Scaffolder::Tool::Sequence do
11
11
  described_class.description.should == desc
12
12
  end
13
13
 
14
- describe "execution when correctly instantiated" do
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+ describe "command line argument" do
15
15
 
16
- before(:each) do
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- entries = [{:name => 'seq1', :nucleotides => 'ATGC'}]
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+ before do
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+ cntg = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
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+ @scf_file, @seq_file = generate_scaffold_files([cntg])
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+ end
20
+
21
+ subject do
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+ Bio::FastaFormat.new(
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+ StringIO.new(
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+ described_class.new(
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+ MockSettings.new(
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+ @scf_file.path,
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+ @seq_file.path,
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+ settings)).execute).string)
29
+ end
18
30
 
19
- @scaffold_file = File.new("scaffold",'w').path
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- @sequence_file = File.new("sequence",'w').path
31
+ describe "empty" do
21
32
 
22
- write_scaffold_file(entries,@scaffold_file)
23
- write_sequence_file(entries,@sequence_file)
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- settings = mock_command_line_settings(@scaffold_file,@sequence_file,{
25
- :definition => nil,:no => nil})
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+ let(:settings) do
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+ {}
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+ end
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+
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+ it "should set the fasta definition" do
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+ subject.definition.should == ""
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+ end
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+
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+ it "should return the expected sequence" do
42
+ subject.seq.should == 'ATGC'
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+ end
26
44
 
27
- tool = described_class.new(settings)
28
- @output = StringIO.new(tool.execute)
29
45
  end
30
46
 
31
- after(:each) do
32
- File.delete @scaffold_file, @sequence_file
47
+ describe "--definition" do
48
+
49
+ let(:settings) do
50
+ {:definition => 'name'}
51
+ end
52
+
53
+ it "should set the fasta definition" do
54
+ subject.definition.should == "name"
55
+ end
56
+
57
+ it "should return the expected sequence" do
58
+ subject.seq.should == 'ATGC'
59
+ end
60
+
33
61
  end
34
62
 
35
- it "should return the expected sequence" do
36
- Bio::FlatFile.auto(@output).first.seq.should == 'ATGC'
63
+ describe "--with-sequence-digest" do
64
+ let(:settings) do
65
+ {:"with-sequence-digest" => true}
66
+ end
67
+
68
+ it "should set the fasta definition" do
69
+ header = "[sha1=627a3d8eb465be91696114803b3410ca92f59cc7]"
70
+ subject.definition.should == header
71
+ end
72
+
73
+ it "should return the expected sequence" do
74
+ subject.seq.should == 'ATGC'
75
+ end
37
76
  end
38
77
 
39
78
  end
@@ -1,4 +1,4 @@
1
- require File.expand_path(File.join(File.dirname(__FILE__),'..','..','spec_helper'))
1
+ require 'spec_helper'
2
2
 
3
3
  describe Scaffolder::Tool::Validate do
4
4
 
@@ -63,7 +63,7 @@ describe Scaffolder::Tool::Validate do
63
63
  end
64
64
 
65
65
  subject do
66
- described_class.new(mock_command_line_settings)
66
+ described_class.new(MockSettings.new)
67
67
  end
68
68
 
69
69
  it "should return an empty array when scaffold is valid" do
@@ -87,7 +87,7 @@ describe Scaffolder::Tool::Validate do
87
87
  describe "scaffold validation with no overlapping inserts" do
88
88
 
89
89
  subject do
90
- validate = described_class.new(mock_command_line_settings)
90
+ validate = described_class.new(MockSettings.new)
91
91
  validate.stubs(:errors).returns([])
92
92
  validate
93
93
  end
@@ -105,7 +105,7 @@ describe Scaffolder::Tool::Validate do
105
105
  describe "returning errors using the errors method" do
106
106
 
107
107
  subject do
108
- validate = described_class.new(mock_command_line_settings)
108
+ validate = described_class.new(MockSettings.new)
109
109
 
110
110
  sequence = stub(:source => :seq1)
111
111
  validate.stubs(:errors).returns([sequence])
@@ -133,7 +133,7 @@ describe Scaffolder::Tool::Validate do
133
133
  describe "the attributes of the error data" do
134
134
 
135
135
  subject do
136
- validate = described_class.new(mock_command_line_settings)
136
+ validate = described_class.new(MockSettings.new)
137
137
  @err = {:open => 1,:close => 2,:source => 'some_insert'}
138
138
 
139
139
  sequence = stub(:source => 'seq1')
@@ -1,4 +1,4 @@
1
- require File.join(File.dirname(__FILE__),'..','spec_helper')
1
+ require 'spec_helper'
2
2
 
3
3
  describe Scaffolder::ToolIndex do
4
4
 
@@ -1,26 +1,26 @@
1
- require File.join(File.dirname(__FILE__),'..','spec_helper')
1
+ require 'spec_helper'
2
2
 
3
3
  describe Scaffolder::Tool do
4
4
 
5
5
  describe "initialisation with attributes" do
6
6
 
7
7
  before(:each) do
8
- @settings = mock_command_line_settings
8
+ @settings = MockSettings.new(:fake_scf,:fake_seq)
9
9
  end
10
10
 
11
11
  subject do
12
12
  Scaffolder::Tool.new(@settings)
13
13
  end
14
14
 
15
- its(:scaffold_file){ should == @settings.scaffold_file }
16
- its(:sequence_file){ should == @settings.sequence_file }
15
+ its(:scaffold_file){ should == @settings.scaf_file }
16
+ its(:sequence_file){ should == @settings.seq_file }
17
17
  its(:settings){ should == @settings }
18
18
  end
19
19
 
20
20
  describe "the run method" do
21
21
 
22
22
  before(:all) do
23
- @settings = mock_command_line_settings
23
+ @settings = MockSettings.new
24
24
  end
25
25
 
26
26
  before(:each) do
@@ -88,28 +88,28 @@ describe Scaffolder::Tool do
88
88
  end
89
89
 
90
90
  it "should raise an error if the sequence file is missing" do
91
- settings = mock_command_line_settings(@scaffold_file,@missing_file)
91
+ settings = MockSettings.new(@scaffold_file,@missing_file)
92
92
  tool = Scaffolder::Tool.new(settings)
93
93
  lambda{ tool.scaffold }.should raise_error(ArgumentError,
94
94
  "Sequence file not found: #{@missing_file}")
95
95
  end
96
96
 
97
97
  it "should raise an error if the sequence file is empty" do
98
- settings = mock_command_line_settings(@scaffold_file,@empty_file)
98
+ settings = MockSettings.new(@scaffold_file,@empty_file)
99
99
  tool = Scaffolder::Tool.new(settings)
100
100
  lambda{ tool.scaffold }.should raise_error(ArgumentError,
101
101
  "Sequence file is empty: #{@empty_file}")
102
102
  end
103
103
 
104
104
  it "should raise an error if the scaffold file is missing" do
105
- settings = mock_command_line_settings(@missing_file,@sequence_file)
105
+ settings = MockSettings.new(@missing_file,@sequence_file)
106
106
  tool = Scaffolder::Tool.new(settings)
107
107
  lambda{ tool.scaffold }.should raise_error(ArgumentError,
108
108
  "Scaffold file not found: #{@missing_file}")
109
109
  end
110
110
 
111
111
  it "should raise an error if the scaffold file is empty" do
112
- settings = mock_command_line_settings(@empty_file,@sequence_file)
112
+ settings = MockSettings.new(@empty_file,@sequence_file)
113
113
  tool = Scaffolder::Tool.new(settings)
114
114
  lambda{ tool.scaffold }.should raise_error(ArgumentError,
115
115
  "Scaffold file is empty: #{@empty_file}")
@@ -119,21 +119,12 @@ describe Scaffolder::Tool do
119
119
  describe "creating the scaffold with the scaffold method" do
120
120
 
121
121
  before(:each) do
122
- entries = [{:name => 'seq1', :nucleotides => 'ATGC'}]
123
-
124
- @scaffold_file = File.new('scaffold','w').path
125
- @sequence_file = File.new('sequence','w').path
126
- write_scaffold_file(entries,@scaffold_file)
127
- write_sequence_file(entries,@sequence_file)
128
- end
129
-
130
- after(:each) do
131
- File.delete @scaffold_file, @sequence_file
122
+ contig = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
123
+ @scf_file, @seq_file = generate_scaffold_files([contig])
132
124
  end
133
125
 
134
126
  subject do
135
- Scaffolder::Tool.new(
136
- mock_command_line_settings(@scaffold_file,@sequence_file))
127
+ Scaffolder::Tool.new(MockSettings.new(@scf_file.path,@seq_file.path))
137
128
  end
138
129
 
139
130
  it "should produce the expected sequence scaffold" do
@@ -4,7 +4,6 @@ $LOAD_PATH.unshift(File.dirname(__FILE__))
4
4
  require 'tempfile'
5
5
  require 'ostruct'
6
6
 
7
- require 'hashie'
8
7
  require 'rspec'
9
8
  require 'fakefs/safe'
10
9
  require 'mocha'
@@ -26,6 +25,7 @@ end
26
25
  RSpec.configure do |config|
27
26
  config.mock_with :mocha
28
27
 
28
+ include Scaffolder::Test
29
29
  include Scaffolder::Test::Helpers
30
30
 
31
31
  def tool_subclasses
@@ -34,18 +34,24 @@ RSpec.configure do |config|
34
34
  end
35
35
  end
36
36
 
37
- def mock_command_line_settings(scaf_file = mock, seq_file = mock, hash_args={})
38
- settings = mock
37
+ class MockSettings
39
38
 
40
- settings.stubs(:rest).returns([scaf_file,seq_file])
41
- settings.stubs(:sequence_file).returns(seq_file)
42
- settings.stubs(:scaffold_file).returns(scaf_file)
39
+ attr :scaf_file
40
+ attr :seq_file
43
41
 
44
- hash_args.each do |key,value|
45
- settings.expects(:[]).with(key).returns(value)
42
+ def initialize(scaf_file = nil, seq_file = nil, command_args = {})
43
+ @scaf_file, @seq_file, = scaf_file, seq_file
44
+ @args = command_args
45
+ end
46
+
47
+ def rest
48
+ [scaf_file,seq_file]
49
+ end
50
+
51
+ def [](arg)
52
+ @args[arg]
46
53
  end
47
54
 
48
- settings
49
55
  end
50
56
 
51
57
  end
@@ -21,6 +21,6 @@ module ExitCodeMatchers
21
21
  end
22
22
  description do
23
23
  "expect block to call exit(#{code})"
24
- end
25
- end
24
+ end
25
+ end
26
26
  end
metadata CHANGED
@@ -1,267 +1,178 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: scaffolder-tools
3
- version: !ruby/object:Gem::Version
4
- hash: 31
5
- prerelease: false
6
- segments:
7
- - 0
8
- - 1
9
- - 2
10
- version: 0.1.2
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.3
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: 2011-01-28 00:00:00 -05:00
19
- default_executable: scaffolder
20
- dependencies:
21
- - !ruby/object:Gem::Dependency
22
- requirement: &id001 !ruby/object:Gem::Requirement
12
+ date: 2011-08-13 00:00:00.000000000Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: configliere
16
+ requirement: &2173650600 !ruby/object:Gem::Requirement
23
17
  none: false
24
- requirements:
18
+ requirements:
25
19
  - - ~>
26
- - !ruby/object:Gem::Version
27
- hash: 9
28
- segments:
29
- - 0
30
- - 1
31
- version: "0.1"
20
+ - !ruby/object:Gem::Version
21
+ version: '0.1'
32
22
  type: :runtime
33
- name: configliere
34
23
  prerelease: false
35
- version_requirements: *id001
36
- - !ruby/object:Gem::Dependency
37
- requirement: &id002 !ruby/object:Gem::Requirement
24
+ version_requirements: *2173650600
25
+ - !ruby/object:Gem::Dependency
26
+ name: bio
27
+ requirement: &2173650020 !ruby/object:Gem::Requirement
38
28
  none: false
39
- requirements:
29
+ requirements:
40
30
  - - ~>
41
- - !ruby/object:Gem::Version
42
- hash: 7
43
- segments:
44
- - 1
45
- - 4
46
- version: "1.4"
31
+ - !ruby/object:Gem::Version
32
+ version: '1.4'
47
33
  type: :runtime
48
- name: bio
49
34
  prerelease: false
50
- version_requirements: *id002
51
- - !ruby/object:Gem::Dependency
52
- requirement: &id003 !ruby/object:Gem::Requirement
35
+ version_requirements: *2173650020
36
+ - !ruby/object:Gem::Dependency
37
+ name: scaffolder
38
+ requirement: &2173649540 !ruby/object:Gem::Requirement
53
39
  none: false
54
- requirements:
40
+ requirements:
55
41
  - - ~>
56
- - !ruby/object:Gem::Version
57
- hash: 3
58
- segments:
59
- - 0
60
- - 4
61
- version: "0.4"
42
+ - !ruby/object:Gem::Version
43
+ version: '0.4'
62
44
  type: :runtime
63
- name: scaffolder
64
45
  prerelease: false
65
- version_requirements: *id003
66
- - !ruby/object:Gem::Dependency
67
- requirement: &id004 !ruby/object:Gem::Requirement
46
+ version_requirements: *2173649540
47
+ - !ruby/object:Gem::Dependency
48
+ name: ronn
49
+ requirement: &2173649060 !ruby/object:Gem::Requirement
68
50
  none: false
69
- requirements:
51
+ requirements:
70
52
  - - ~>
71
- - !ruby/object:Gem::Version
72
- hash: 5
73
- segments:
74
- - 0
75
- - 7
76
- version: "0.7"
53
+ - !ruby/object:Gem::Version
54
+ version: '0.7'
77
55
  type: :runtime
78
- name: ronn
79
56
  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
57
+ version_requirements: *2173649060
58
+ - !ruby/object:Gem::Dependency
93
59
  name: bundler
94
- prerelease: false
95
- version_requirements: *id005
96
- - !ruby/object:Gem::Dependency
97
- requirement: &id006 !ruby/object:Gem::Requirement
60
+ requirement: &2173648520 !ruby/object:Gem::Requirement
98
61
  none: false
99
- requirements:
62
+ requirements:
100
63
  - - ~>
101
- - !ruby/object:Gem::Version
102
- hash: 5
103
- segments:
104
- - 1
105
- - 5
106
- version: "1.5"
64
+ - !ruby/object:Gem::Version
65
+ version: '1.0'
107
66
  type: :development
108
- name: jeweler
109
67
  prerelease: false
110
- version_requirements: *id006
111
- - !ruby/object:Gem::Dependency
112
- requirement: &id007 !ruby/object:Gem::Requirement
68
+ version_requirements: *2173648520
69
+ - !ruby/object:Gem::Dependency
70
+ name: jeweler
71
+ requirement: &2173647960 !ruby/object:Gem::Requirement
113
72
  none: false
114
- requirements:
73
+ requirements:
115
74
  - - ~>
116
- - !ruby/object:Gem::Version
117
- hash: 5
118
- segments:
119
- - 2
120
- - 3
121
- - 3
122
- version: 2.3.3
75
+ - !ruby/object:Gem::Version
76
+ version: '1.5'
123
77
  type: :development
124
- name: gherkin
125
78
  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
79
+ version_requirements: *2173647960
80
+ - !ruby/object:Gem::Dependency
139
81
  name: rspec
140
- prerelease: false
141
- version_requirements: *id008
142
- - !ruby/object:Gem::Dependency
143
- requirement: &id009 !ruby/object:Gem::Requirement
82
+ requirement: &2173647360 !ruby/object:Gem::Requirement
144
83
  none: false
145
- requirements:
84
+ requirements:
146
85
  - - ~>
147
- - !ruby/object:Gem::Version
148
- hash: 31
149
- segments:
150
- - 0
151
- - 10
152
- version: "0.10"
86
+ - !ruby/object:Gem::Version
87
+ version: '2.4'
153
88
  type: :development
154
- name: cucumber
155
89
  prerelease: false
156
- version_requirements: *id009
157
- - !ruby/object:Gem::Dependency
158
- requirement: &id010 !ruby/object:Gem::Requirement
90
+ version_requirements: *2173647360
91
+ - !ruby/object:Gem::Dependency
92
+ name: cucumber
93
+ requirement: &2173646840 !ruby/object:Gem::Requirement
159
94
  none: false
160
- requirements:
95
+ requirements:
161
96
  - - ~>
162
- - !ruby/object:Gem::Version
163
- hash: 15
164
- segments:
165
- - 0
166
- - 2
167
- version: "0.2"
97
+ - !ruby/object:Gem::Version
98
+ version: '0.10'
168
99
  type: :development
169
- name: fakefs
170
100
  prerelease: false
171
- version_requirements: *id010
172
- - !ruby/object:Gem::Dependency
173
- requirement: &id011 !ruby/object:Gem::Requirement
101
+ version_requirements: *2173646840
102
+ - !ruby/object:Gem::Dependency
103
+ name: fakefs
104
+ requirement: &2173646340 !ruby/object:Gem::Requirement
174
105
  none: false
175
- requirements:
106
+ requirements:
176
107
  - - ~>
177
- - !ruby/object:Gem::Version
178
- hash: 15
179
- segments:
180
- - 0
181
- - 2
182
- version: "0.2"
108
+ - !ruby/object:Gem::Version
109
+ version: '0.2'
183
110
  type: :development
184
- name: aruba
185
111
  prerelease: false
186
- version_requirements: *id011
187
- - !ruby/object:Gem::Dependency
188
- requirement: &id012 !ruby/object:Gem::Requirement
112
+ version_requirements: *2173646340
113
+ - !ruby/object:Gem::Dependency
114
+ name: aruba
115
+ requirement: &2173645780 !ruby/object:Gem::Requirement
189
116
  none: false
190
- requirements:
117
+ requirements:
191
118
  - - ~>
192
- - !ruby/object:Gem::Version
193
- hash: 25
194
- segments:
195
- - 0
196
- - 9
197
- version: "0.9"
119
+ - !ruby/object:Gem::Version
120
+ version: '0.2'
198
121
  type: :development
199
- name: mocha
200
122
  prerelease: false
201
- version_requirements: *id012
202
- - !ruby/object:Gem::Dependency
203
- requirement: &id013 !ruby/object:Gem::Requirement
123
+ version_requirements: *2173645780
124
+ - !ruby/object:Gem::Dependency
125
+ name: mocha
126
+ requirement: &2173645240 !ruby/object:Gem::Requirement
204
127
  none: false
205
- requirements:
128
+ requirements:
206
129
  - - ~>
207
- - !ruby/object:Gem::Version
208
- hash: 3
209
- segments:
210
- - 0
211
- - 4
212
- version: "0.4"
130
+ - !ruby/object:Gem::Version
131
+ version: '0.9'
213
132
  type: :development
214
- name: hashie
215
133
  prerelease: false
216
- version_requirements: *id013
217
- - !ruby/object:Gem::Dependency
218
- requirement: &id014 !ruby/object:Gem::Requirement
134
+ version_requirements: *2173645240
135
+ - !ruby/object:Gem::Dependency
136
+ name: yard
137
+ requirement: &2173644660 !ruby/object:Gem::Requirement
219
138
  none: false
220
- requirements:
139
+ requirements:
221
140
  - - ~>
222
- - !ruby/object:Gem::Version
223
- hash: 7
224
- segments:
225
- - 0
226
- - 6
227
- version: "0.6"
141
+ - !ruby/object:Gem::Version
142
+ version: '0.6'
228
143
  type: :development
229
- name: yard
230
144
  prerelease: false
231
- version_requirements: *id014
232
- - !ruby/object:Gem::Dependency
233
- requirement: &id015 !ruby/object:Gem::Requirement
145
+ version_requirements: *2173644660
146
+ - !ruby/object:Gem::Dependency
147
+ name: scaffolder-test-helpers
148
+ requirement: &2173644100 !ruby/object:Gem::Requirement
234
149
  none: false
235
- requirements:
150
+ requirements:
236
151
  - - ~>
237
- - !ruby/object:Gem::Version
238
- hash: 9
239
- segments:
240
- - 0
241
- - 1
242
- version: "0.1"
152
+ - !ruby/object:Gem::Version
153
+ version: '0.4'
243
154
  type: :development
244
- name: scaffolder-test-helpers
245
155
  prerelease: false
246
- version_requirements: *id015
156
+ version_requirements: *2173644100
247
157
  description: Binary to use with scaffolder genome scaffolds
248
- email: mail@michaelbarton.me.uk
249
- executables:
158
+ email: mail@next.gs
159
+ executables:
250
160
  - scaffolder
251
161
  extensions: []
252
-
253
- extra_rdoc_files:
162
+ extra_rdoc_files:
254
163
  - LICENSE.txt
255
164
  - README.rdoc
256
- files:
165
+ files:
257
166
  - .document
258
167
  - .rspec
168
+ - .travis.yml
259
169
  - Gemfile
260
170
  - LICENSE.txt
261
171
  - README.rdoc
262
172
  - Rakefile
263
173
  - VERSION
264
174
  - bin/scaffolder
175
+ - features/error_checking.feature
265
176
  - features/help.feature
266
177
  - features/sequence.feature
267
178
  - features/step_definitions/scaffolder-tools.rb
@@ -273,6 +184,7 @@ files:
273
184
  - lib/scaffolder/tool/sequence.rb
274
185
  - lib/scaffolder/tool/validate.rb
275
186
  - lib/scaffolder/tool_index.rb
187
+ - man/scaffolder-format.7.ronn
276
188
  - man/scaffolder-help.1.ronn
277
189
  - man/scaffolder-sequence.1.ronn
278
190
  - man/scaffolder-validate.1.ronn
@@ -285,41 +197,35 @@ files:
285
197
  - spec/scaffolder/tool_spec.rb
286
198
  - spec/spec_helper.rb
287
199
  - spec/support/exit_code_matcher.rb
288
- has_rdoc: true
289
- homepage: http://www.michaelbarton.me.uk/projects/scaffolder/
290
- licenses:
200
+ homepage: http://next.gs
201
+ licenses:
291
202
  - MIT
292
203
  post_install_message:
293
204
  rdoc_options: []
294
-
295
- require_paths:
205
+ require_paths:
296
206
  - lib
297
- required_ruby_version: !ruby/object:Gem::Requirement
207
+ required_ruby_version: !ruby/object:Gem::Requirement
298
208
  none: false
299
- requirements:
300
- - - ">="
301
- - !ruby/object:Gem::Version
302
- hash: 3
303
- segments:
209
+ requirements:
210
+ - - ! '>='
211
+ - !ruby/object:Gem::Version
212
+ version: '0'
213
+ segments:
304
214
  - 0
305
- version: "0"
306
- required_rubygems_version: !ruby/object:Gem::Requirement
215
+ hash: 2501104196888492226
216
+ required_rubygems_version: !ruby/object:Gem::Requirement
307
217
  none: false
308
- requirements:
309
- - - ">="
310
- - !ruby/object:Gem::Version
311
- hash: 3
312
- segments:
313
- - 0
314
- version: "0"
218
+ requirements:
219
+ - - ! '>='
220
+ - !ruby/object:Gem::Version
221
+ version: '0'
315
222
  requirements: []
316
-
317
223
  rubyforge_project:
318
- rubygems_version: 1.3.7
224
+ rubygems_version: 1.8.6
319
225
  signing_key:
320
226
  specification_version: 3
321
227
  summary: Tools for manipulating genome scaffolds
322
- test_files:
228
+ test_files:
323
229
  - spec/scaffolder/binary_helper_spec.rb
324
230
  - spec/scaffolder/tool/help_spec.rb
325
231
  - spec/scaffolder/tool/sequence_spec.rb