quorum 0.3.0 → 0.3.1
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- data/Gemfile.lock +58 -58
- data/HISTORY.md +4 -0
- data/README.rdoc +31 -31
- data/app/assets/javascripts/quorum/jobs.js +2 -2
- data/app/assets/javascripts/quorum/quorum.js +55 -55
- data/app/assets/stylesheets/quorum/application.css +23 -23
- data/app/assets/stylesheets/quorum/jquery-ui-1.8.16.custom.css +5 -5
- data/app/controllers/quorum/jobs_controller.rb +7 -7
- data/app/models/quorum/blastn_job.rb +1 -1
- data/app/models/quorum/blastp_job.rb +1 -1
- data/app/models/quorum/blastx_job.rb +1 -1
- data/app/models/quorum/job.rb +19 -19
- data/app/models/quorum/tblastn_job.rb +1 -1
- data/app/views/quorum/jobs/form/_blastn_form.html.erb +7 -7
- data/app/views/quorum/jobs/form/_blastp_form.html.erb +7 -7
- data/app/views/quorum/jobs/form/_blastx_form.html.erb +7 -7
- data/app/views/quorum/jobs/form/_tblastn_form.html.erb +7 -7
- data/app/views/quorum/jobs/new.html.erb +9 -9
- data/app/views/quorum/jobs/show.html.erb +7 -7
- data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb +3 -3
- data/app/views/quorum/jobs/templates/_blast_template.html.erb +4 -4
- data/lib/generators/quorum/install_generator.rb +3 -3
- data/lib/generators/quorum/views_generator.rb +7 -6
- data/lib/generators/templates/README +3 -3
- data/lib/generators/templates/blast.rb +7 -7
- data/lib/generators/templates/blast_db.rb +6 -6
- data/lib/generators/templates/fetch +3 -3
- data/lib/generators/templates/quorum_initializer.rb +1 -1
- data/lib/generators/templates/quorum_settings.yml +1 -1
- data/lib/generators/templates/search +8 -8
- data/lib/generators/templates/trollop.rb +4 -4
- data/lib/quorum/sequence.rb +6 -6
- data/lib/quorum/version.rb +1 -1
- data/lib/quorum.rb +1 -1
- data/lib/tasks/blastdb/build_blast_db.rb +7 -7
- data/lib/tasks/quorum_tasks.rake +6 -6
- data/lib/workers/quorum.rb +2 -2
- data/quorum.gemspec +1 -1
- data/spec/dummy/quorum/blastdb/test.nin +0 -0
- data/spec/dummy/quorum/blastdb/test.pin +0 -0
- data/spec/javascripts/fixtures/quorum_search_form.html +8 -8
- data/spec/javascripts/quorum_spec.js +12 -12
- data/spec/javascripts/string_spec.js +2 -2
- data/spec/models/blastn_job_report_spec.rb +3 -3
- data/spec/models/blastp_job_report_spec.rb +3 -3
- data/spec/models/blastx_job_report_spec.rb +3 -3
- data/spec/models/job_spec.rb +1 -1
- data/spec/models/tblastn_job_report_spec.rb +3 -3
- data/spec/quorum/quorum_sequence_spec.rb +1 -1
- data/spec/requests/jobs_spec.rb +12 -11
- data/spec/spec_helper.rb +1 -1
- data/spec/tasks/blastdb_rake_spec.rb +5 -5
- data/spec/templates/blast_spec.rb +5 -5
- data/vendor/assets/javascripts/jquery.autohint.js +16 -16
- data/vendor/assets/javascripts/jquery.tipsy.js +33 -33
- metadata +96 -31
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: quorum
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version: !ruby/object:Gem::Version
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version: 0.3.
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version: 0.3.1
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prerelease:
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platform: ruby
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authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-
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date: 2012-04-02 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rails
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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version: '3.1'
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type: :runtime
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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version: '3.1'
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name: jquery-rails
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -32,10 +37,15 @@ dependencies:
|
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version: '0'
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|
type: :runtime
|
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|
prerelease: false
|
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-
version_requirements:
|
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
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+
requirements:
|
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+
- - ! '>='
|
44
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+
- !ruby/object:Gem::Version
|
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+
version: '0'
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|
- !ruby/object:Gem::Dependency
|
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|
name: net-ssh
|
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|
-
requirement:
|
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+
requirement: !ruby/object:Gem::Requirement
|
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|
none: false
|
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|
requirements:
|
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|
- - ~>
|
@@ -43,10 +53,15 @@ dependencies:
|
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version: 2.3.0
|
44
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|
type: :runtime
|
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prerelease: false
|
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-
version_requirements:
|
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+
version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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- - ~>
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- !ruby/object:Gem::Version
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version: 2.3.0
|
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name: resque
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requirement:
|
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
|
@@ -54,10 +69,15 @@ dependencies:
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version: 1.19.0
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type: :runtime
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.19.0
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- !ruby/object:Gem::Dependency
|
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name: resque-result
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requirement:
|
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
|
@@ -65,10 +85,15 @@ dependencies:
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version: 1.0.1
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type: :runtime
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prerelease: false
|
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version_requirements:
|
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version_requirements: !ruby/object:Gem::Requirement
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none: false
|
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requirements:
|
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+
- - ~>
|
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- !ruby/object:Gem::Version
|
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version: 1.0.1
|
69
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|
- !ruby/object:Gem::Dependency
|
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|
name: bio-blastxmlparser
|
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|
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requirement:
|
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requirement: !ruby/object:Gem::Requirement
|
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|
none: false
|
73
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|
requirements:
|
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|
- - ~>
|
@@ -76,10 +101,15 @@ dependencies:
|
|
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version: 1.0.1
|
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|
type: :runtime
|
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prerelease: false
|
79
|
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version_requirements:
|
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
|
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requirements:
|
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+
- - ~>
|
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- !ruby/object:Gem::Version
|
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|
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version: 1.0.1
|
80
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|
- !ruby/object:Gem::Dependency
|
81
111
|
name: mysql2
|
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|
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requirement:
|
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+
requirement: !ruby/object:Gem::Requirement
|
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|
none: false
|
84
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|
requirements:
|
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|
- - ~>
|
@@ -87,10 +117,15 @@ dependencies:
|
|
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version: 0.3.11
|
88
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|
type: :development
|
89
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|
prerelease: false
|
90
|
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version_requirements:
|
120
|
+
version_requirements: !ruby/object:Gem::Requirement
|
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none: false
|
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|
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requirements:
|
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|
+
- - ~>
|
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- !ruby/object:Gem::Version
|
125
|
+
version: 0.3.11
|
91
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|
- !ruby/object:Gem::Dependency
|
92
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|
name: rspec-rails
|
93
|
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requirement:
|
128
|
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requirement: !ruby/object:Gem::Requirement
|
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|
none: false
|
95
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|
requirements:
|
96
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|
- - ~>
|
@@ -98,10 +133,15 @@ dependencies:
|
|
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version: '2.6'
|
99
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|
type: :development
|
100
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|
prerelease: false
|
101
|
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version_requirements:
|
136
|
+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
|
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|
+
requirements:
|
139
|
+
- - ~>
|
140
|
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- !ruby/object:Gem::Version
|
141
|
+
version: '2.6'
|
102
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|
- !ruby/object:Gem::Dependency
|
103
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|
name: resque_spec
|
104
|
-
requirement:
|
144
|
+
requirement: !ruby/object:Gem::Requirement
|
105
145
|
none: false
|
106
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|
requirements:
|
107
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|
- - ~>
|
@@ -109,10 +149,15 @@ dependencies:
|
|
109
149
|
version: '0.8'
|
110
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|
type: :development
|
111
151
|
prerelease: false
|
112
|
-
version_requirements:
|
152
|
+
version_requirements: !ruby/object:Gem::Requirement
|
153
|
+
none: false
|
154
|
+
requirements:
|
155
|
+
- - ~>
|
156
|
+
- !ruby/object:Gem::Version
|
157
|
+
version: '0.8'
|
113
158
|
- !ruby/object:Gem::Dependency
|
114
159
|
name: capybara
|
115
|
-
requirement:
|
160
|
+
requirement: !ruby/object:Gem::Requirement
|
116
161
|
none: false
|
117
162
|
requirements:
|
118
163
|
- - ~>
|
@@ -120,10 +165,15 @@ dependencies:
|
|
120
165
|
version: '1.1'
|
121
166
|
type: :development
|
122
167
|
prerelease: false
|
123
|
-
version_requirements:
|
168
|
+
version_requirements: !ruby/object:Gem::Requirement
|
169
|
+
none: false
|
170
|
+
requirements:
|
171
|
+
- - ~>
|
172
|
+
- !ruby/object:Gem::Version
|
173
|
+
version: '1.1'
|
124
174
|
- !ruby/object:Gem::Dependency
|
125
175
|
name: database_cleaner
|
126
|
-
requirement:
|
176
|
+
requirement: !ruby/object:Gem::Requirement
|
127
177
|
none: false
|
128
178
|
requirements:
|
129
179
|
- - ~>
|
@@ -131,10 +181,15 @@ dependencies:
|
|
131
181
|
version: '0.6'
|
132
182
|
type: :development
|
133
183
|
prerelease: false
|
134
|
-
version_requirements:
|
184
|
+
version_requirements: !ruby/object:Gem::Requirement
|
185
|
+
none: false
|
186
|
+
requirements:
|
187
|
+
- - ~>
|
188
|
+
- !ruby/object:Gem::Version
|
189
|
+
version: '0.6'
|
135
190
|
- !ruby/object:Gem::Dependency
|
136
191
|
name: factory_girl_rails
|
137
|
-
requirement:
|
192
|
+
requirement: !ruby/object:Gem::Requirement
|
138
193
|
none: false
|
139
194
|
requirements:
|
140
195
|
- - ~>
|
@@ -142,10 +197,15 @@ dependencies:
|
|
142
197
|
version: '1.2'
|
143
198
|
type: :development
|
144
199
|
prerelease: false
|
145
|
-
version_requirements:
|
200
|
+
version_requirements: !ruby/object:Gem::Requirement
|
201
|
+
none: false
|
202
|
+
requirements:
|
203
|
+
- - ~>
|
204
|
+
- !ruby/object:Gem::Version
|
205
|
+
version: '1.2'
|
146
206
|
- !ruby/object:Gem::Dependency
|
147
207
|
name: jasmine
|
148
|
-
requirement:
|
208
|
+
requirement: !ruby/object:Gem::Requirement
|
149
209
|
none: false
|
150
210
|
requirements:
|
151
211
|
- - ~>
|
@@ -153,7 +213,12 @@ dependencies:
|
|
153
213
|
version: '1.1'
|
154
214
|
type: :development
|
155
215
|
prerelease: false
|
156
|
-
version_requirements:
|
216
|
+
version_requirements: !ruby/object:Gem::Requirement
|
217
|
+
none: false
|
218
|
+
requirements:
|
219
|
+
- - ~>
|
220
|
+
- !ruby/object:Gem::Version
|
221
|
+
version: '1.1'
|
157
222
|
description: Flexible bioinformatics search tool.
|
158
223
|
email:
|
159
224
|
- kas@ncgr.org
|
@@ -369,7 +434,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
369
434
|
version: '0'
|
370
435
|
segments:
|
371
436
|
- 0
|
372
|
-
hash:
|
437
|
+
hash: -2365568155334163580
|
373
438
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
374
439
|
none: false
|
375
440
|
requirements:
|
@@ -378,10 +443,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
378
443
|
version: '0'
|
379
444
|
segments:
|
380
445
|
- 0
|
381
|
-
hash:
|
446
|
+
hash: -2365568155334163580
|
382
447
|
requirements: []
|
383
448
|
rubyforge_project:
|
384
|
-
rubygems_version: 1.8.
|
449
|
+
rubygems_version: 1.8.21
|
385
450
|
signing_key:
|
386
451
|
specification_version: 3
|
387
452
|
summary: Flexible bioinformatics search tool.
|