quorum 0.3.3 → 0.4.0
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- data/Gemfile.lock +42 -48
- data/HISTORY.md +11 -0
- data/app/assets/javascripts/quorum/quorum.js +8 -5
- data/db/migrate/20120807202555_add_gaps_to_blast_reports.rb +8 -0
- data/lib/generators/templates/blast.rb +76 -40
- data/lib/quorum/version.rb +1 -1
- data/quorum.gemspec +6 -7
- data/spec/data/fake_seq.txt +2 -0
- data/spec/data/nucl_prot_seqs.txt +15 -0
- data/spec/data/tmp/test.tgz +0 -0
- data/spec/dummy/config/initializers/quorum_initializer.rb +1 -1
- data/spec/dummy/config/quorum_settings.yml +5 -9
- data/spec/dummy/db/schema.rb +23 -19
- data/spec/dummy/quorum/bin/fetch +3 -3
- data/spec/dummy/quorum/bin/search +8 -8
- data/spec/dummy/quorum/blastdb/test/contigs.fa +13 -0
- data/spec/dummy/quorum/blastdb/test/peptides.fa +2 -0
- data/spec/dummy/quorum/blastdb/test.nhd +1 -0
- data/spec/dummy/quorum/blastdb/test.nhi +0 -0
- data/spec/dummy/quorum/blastdb/test.nhr +0 -0
- data/spec/dummy/quorum/blastdb/test.nin +0 -0
- data/spec/dummy/quorum/blastdb/test.nog +0 -0
- data/spec/dummy/quorum/blastdb/test.nsd +1 -0
- data/spec/dummy/quorum/blastdb/test.nsi +0 -0
- data/spec/dummy/quorum/blastdb/test.nsq +0 -0
- data/spec/dummy/quorum/blastdb/test.phd +1 -0
- data/spec/dummy/quorum/blastdb/test.phi +0 -0
- data/spec/dummy/quorum/blastdb/test.phr +0 -0
- data/spec/dummy/quorum/blastdb/test.pin +0 -0
- data/spec/dummy/quorum/blastdb/test.pog +0 -0
- data/spec/dummy/quorum/blastdb/test.psd +1 -0
- data/spec/dummy/quorum/blastdb/test.psi +0 -0
- data/spec/dummy/quorum/blastdb/test.psq +0 -0
- data/spec/dummy/quorum/lib/fetch_tools/blast_db.rb +6 -6
- data/spec/dummy/quorum/lib/logger.rb +4 -4
- data/spec/dummy/quorum/lib/search_tools/blast.rb +76 -40
- data/spec/dummy/quorum/lib/trollop.rb +4 -4
- data/spec/javascripts/fixtures/formatted_sequence.html +1 -1
- data/spec/javascripts/quorum_spec.js +8 -6
- data/spec/requests/jobs_spec.rb +13 -3
- data/spec/spec_helper.rb +0 -4
- data/spec/templates/blast_spec.rb +53 -3
- metadata +17 -31
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: quorum
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.4.0
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -9,7 +9,7 @@ authors:
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|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2012-
|
12
|
+
date: 2012-08-10 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: rails
|
@@ -66,7 +66,7 @@ dependencies:
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|
66
66
|
requirements:
|
67
67
|
- - ~>
|
68
68
|
- !ruby/object:Gem::Version
|
69
|
-
version: 1.
|
69
|
+
version: 1.20.0
|
70
70
|
type: :runtime
|
71
71
|
prerelease: false
|
72
72
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -74,7 +74,7 @@ dependencies:
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|
74
74
|
requirements:
|
75
75
|
- - ~>
|
76
76
|
- !ruby/object:Gem::Version
|
77
|
-
version: 1.
|
77
|
+
version: 1.20.0
|
78
78
|
- !ruby/object:Gem::Dependency
|
79
79
|
name: resque-result
|
80
80
|
requirement: !ruby/object:Gem::Requirement
|
@@ -98,7 +98,7 @@ dependencies:
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|
98
98
|
requirements:
|
99
99
|
- - ~>
|
100
100
|
- !ruby/object:Gem::Version
|
101
|
-
version: 1.0
|
101
|
+
version: 1.1.0
|
102
102
|
type: :runtime
|
103
103
|
prerelease: false
|
104
104
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -106,7 +106,7 @@ dependencies:
|
|
106
106
|
requirements:
|
107
107
|
- - ~>
|
108
108
|
- !ruby/object:Gem::Version
|
109
|
-
version: 1.0
|
109
|
+
version: 1.1.0
|
110
110
|
- !ruby/object:Gem::Dependency
|
111
111
|
name: mysql2
|
112
112
|
requirement: !ruby/object:Gem::Requirement
|
@@ -130,7 +130,7 @@ dependencies:
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|
130
130
|
requirements:
|
131
131
|
- - ~>
|
132
132
|
- !ruby/object:Gem::Version
|
133
|
-
version: '2.
|
133
|
+
version: '2.11'
|
134
134
|
type: :development
|
135
135
|
prerelease: false
|
136
136
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -138,7 +138,7 @@ dependencies:
|
|
138
138
|
requirements:
|
139
139
|
- - ~>
|
140
140
|
- !ruby/object:Gem::Version
|
141
|
-
version: '2.
|
141
|
+
version: '2.11'
|
142
142
|
- !ruby/object:Gem::Dependency
|
143
143
|
name: resque_spec
|
144
144
|
requirement: !ruby/object:Gem::Requirement
|
@@ -146,7 +146,7 @@ dependencies:
|
|
146
146
|
requirements:
|
147
147
|
- - ~>
|
148
148
|
- !ruby/object:Gem::Version
|
149
|
-
version: '0.
|
149
|
+
version: '0.12'
|
150
150
|
type: :development
|
151
151
|
prerelease: false
|
152
152
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -154,7 +154,7 @@ dependencies:
|
|
154
154
|
requirements:
|
155
155
|
- - ~>
|
156
156
|
- !ruby/object:Gem::Version
|
157
|
-
version: '0.
|
157
|
+
version: '0.12'
|
158
158
|
- !ruby/object:Gem::Dependency
|
159
159
|
name: capybara
|
160
160
|
requirement: !ruby/object:Gem::Requirement
|
@@ -178,7 +178,7 @@ dependencies:
|
|
178
178
|
requirements:
|
179
179
|
- - ~>
|
180
180
|
- !ruby/object:Gem::Version
|
181
|
-
version: '0.
|
181
|
+
version: '0.8'
|
182
182
|
type: :development
|
183
183
|
prerelease: false
|
184
184
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -186,9 +186,9 @@ dependencies:
|
|
186
186
|
requirements:
|
187
187
|
- - ~>
|
188
188
|
- !ruby/object:Gem::Version
|
189
|
-
version: '0.
|
189
|
+
version: '0.8'
|
190
190
|
- !ruby/object:Gem::Dependency
|
191
|
-
name:
|
191
|
+
name: jasmine
|
192
192
|
requirement: !ruby/object:Gem::Requirement
|
193
193
|
none: false
|
194
194
|
requirements:
|
@@ -203,22 +203,6 @@ dependencies:
|
|
203
203
|
- - ~>
|
204
204
|
- !ruby/object:Gem::Version
|
205
205
|
version: '1.2'
|
206
|
-
- !ruby/object:Gem::Dependency
|
207
|
-
name: jasmine
|
208
|
-
requirement: !ruby/object:Gem::Requirement
|
209
|
-
none: false
|
210
|
-
requirements:
|
211
|
-
- - ~>
|
212
|
-
- !ruby/object:Gem::Version
|
213
|
-
version: '1.1'
|
214
|
-
type: :development
|
215
|
-
prerelease: false
|
216
|
-
version_requirements: !ruby/object:Gem::Requirement
|
217
|
-
none: false
|
218
|
-
requirements:
|
219
|
-
- - ~>
|
220
|
-
- !ruby/object:Gem::Version
|
221
|
-
version: '1.1'
|
222
206
|
description: Flexible bioinformatics search tool.
|
223
207
|
email:
|
224
208
|
- kas@ncgr.org
|
@@ -295,6 +279,7 @@ files:
|
|
295
279
|
- db/migrate/20111031204922_create_blastp_job_reports.rb
|
296
280
|
- db/migrate/20111031204941_create_tblastn_job_reports.rb
|
297
281
|
- db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb
|
282
|
+
- db/migrate/20120807202555_add_gaps_to_blast_reports.rb
|
298
283
|
- lib/generators/quorum/images_generator.rb
|
299
284
|
- lib/generators/quorum/install_generator.rb
|
300
285
|
- lib/generators/quorum/styles_generator.rb
|
@@ -321,6 +306,7 @@ files:
|
|
321
306
|
- lib/workers/quorum.rb
|
322
307
|
- quorum.gemspec
|
323
308
|
- script/rails
|
309
|
+
- spec/data/fake_seq.txt
|
324
310
|
- spec/data/nucl_prot_seqs.txt
|
325
311
|
- spec/data/nucl_seqs.txt
|
326
312
|
- spec/data/nucl_seqs_lower.txt
|
@@ -440,7 +426,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
440
426
|
version: '0'
|
441
427
|
segments:
|
442
428
|
- 0
|
443
|
-
hash: -
|
429
|
+
hash: -3860118891920834630
|
444
430
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
445
431
|
none: false
|
446
432
|
requirements:
|
@@ -449,7 +435,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
449
435
|
version: '0'
|
450
436
|
segments:
|
451
437
|
- 0
|
452
|
-
hash: -
|
438
|
+
hash: -3860118891920834630
|
453
439
|
requirements: []
|
454
440
|
rubyforge_project:
|
455
441
|
rubygems_version: 1.8.24
|