miga-base 0.2.0.6 → 0.2.0.7
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- checksums.yaml +4 -4
- data/Gemfile +3 -0
- data/LICENSE +201 -0
- data/README.md +17 -335
- data/Rakefile +31 -0
- data/actions/add_result +2 -5
- data/actions/add_taxonomy +4 -7
- data/actions/create_dataset +5 -6
- data/actions/create_project +2 -5
- data/actions/daemon +2 -5
- data/actions/download_dataset +88 -58
- data/actions/find_datasets +36 -38
- data/actions/import_datasets +2 -5
- data/actions/index_taxonomy +2 -5
- data/actions/list_datasets +47 -49
- data/actions/list_files +7 -11
- data/actions/unlink_dataset +2 -5
- data/bin/miga +1 -1
- data/lib/miga/common.rb +132 -0
- data/lib/miga/daemon.rb +229 -168
- data/lib/miga/dataset.rb +354 -277
- data/lib/miga/gui.rb +346 -269
- data/lib/miga/metadata.rb +115 -71
- data/lib/miga/project.rb +361 -259
- data/lib/miga/remote_dataset.rb +200 -148
- data/lib/miga/result.rb +150 -99
- data/lib/miga/tax_index.rb +124 -67
- data/lib/miga/taxonomy.rb +129 -100
- data/lib/miga/version.rb +57 -0
- data/lib/miga.rb +2 -77
- data/scripts/_distances_noref_nomulti.bash +2 -0
- data/scripts/_distances_ref_nomulti.bash +2 -0
- data/scripts/aai_distances.bash +1 -0
- data/scripts/ani_distances.bash +1 -0
- data/scripts/assembly.bash +1 -0
- data/scripts/cds.bash +1 -0
- data/scripts/clade_finding.bash +17 -1
- data/scripts/distances.bash +1 -0
- data/scripts/essential_genes.bash +1 -0
- data/scripts/haai_distances.bash +1 -0
- data/scripts/init.bash +2 -0
- data/scripts/mytaxa.bash +1 -0
- data/scripts/mytaxa_scan.bash +1 -0
- data/scripts/ogs.bash +1 -0
- data/scripts/read_quality.bash +1 -0
- data/scripts/ssu.bash +1 -0
- data/scripts/subclades.bash +1 -0
- data/scripts/trimmed_fasta.bash +1 -0
- data/scripts/trimmed_reads.bash +1 -0
- data/test/common_test.rb +82 -0
- data/test/daemon_test.rb +53 -0
- data/test/dataset_test.rb +156 -0
- data/test/jruby_gui_test.rb +20 -0
- data/test/metadata_test.rb +48 -0
- data/test/project_test.rb +54 -0
- data/test/remote_dataset_test.rb +41 -0
- data/test/tax_index_test.rb +44 -0
- data/test/taxonomy_test.rb +36 -0
- data/test/test_helper.rb +32 -0
- metadata +53 -38
metadata
CHANGED
@@ -1,99 +1,99 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: miga-base
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.2.0.
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4
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+
version: 0.2.0.7
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Luis M. Rodriguez-R
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8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
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11
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-
date:
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11
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+
date: 2016-04-13 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: rest-client
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15
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requirement: !ruby/object:Gem::Requirement
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16
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requirements:
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17
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-
- - ~>
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17
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+
- - "~>"
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18
18
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- !ruby/object:Gem::Version
|
19
19
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version: '1.7'
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20
20
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type: :runtime
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21
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prerelease: false
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22
22
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version_requirements: !ruby/object:Gem::Requirement
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23
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requirements:
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24
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-
- - ~>
|
24
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+
- - "~>"
|
25
25
|
- !ruby/object:Gem::Version
|
26
26
|
version: '1.7'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: sqlite3
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- - ~>
|
31
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+
- - "~>"
|
32
32
|
- !ruby/object:Gem::Version
|
33
33
|
version: '1.3'
|
34
34
|
type: :runtime
|
35
35
|
prerelease: false
|
36
36
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version_requirements: !ruby/object:Gem::Requirement
|
37
37
|
requirements:
|
38
|
-
- - ~>
|
38
|
+
- - "~>"
|
39
39
|
- !ruby/object:Gem::Version
|
40
40
|
version: '1.3'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
42
|
name: daemons
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
|
-
- - ~>
|
45
|
+
- - "~>"
|
46
46
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- !ruby/object:Gem::Version
|
47
47
|
version: '1.2'
|
48
48
|
type: :runtime
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
|
-
- - ~>
|
52
|
+
- - "~>"
|
53
53
|
- !ruby/object:Gem::Version
|
54
54
|
version: '1.2'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
56
|
name: json
|
57
57
|
requirement: !ruby/object:Gem::Requirement
|
58
58
|
requirements:
|
59
|
-
- - ~>
|
59
|
+
- - "~>"
|
60
60
|
- !ruby/object:Gem::Version
|
61
61
|
version: '1.8'
|
62
62
|
type: :runtime
|
63
63
|
prerelease: false
|
64
64
|
version_requirements: !ruby/object:Gem::Requirement
|
65
65
|
requirements:
|
66
|
-
- - ~>
|
66
|
+
- - "~>"
|
67
67
|
- !ruby/object:Gem::Version
|
68
68
|
version: '1.8'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
|
name: rake
|
71
71
|
requirement: !ruby/object:Gem::Requirement
|
72
72
|
requirements:
|
73
|
-
- -
|
73
|
+
- - "~>"
|
74
74
|
- !ruby/object:Gem::Version
|
75
|
-
version: '
|
75
|
+
version: '11'
|
76
76
|
type: :development
|
77
77
|
prerelease: false
|
78
78
|
version_requirements: !ruby/object:Gem::Requirement
|
79
79
|
requirements:
|
80
|
-
- -
|
80
|
+
- - "~>"
|
81
81
|
- !ruby/object:Gem::Version
|
82
|
-
version: '
|
82
|
+
version: '11'
|
83
83
|
- !ruby/object:Gem::Dependency
|
84
84
|
name: test-unit
|
85
85
|
requirement: !ruby/object:Gem::Requirement
|
86
86
|
requirements:
|
87
|
-
- -
|
87
|
+
- - "~>"
|
88
88
|
- !ruby/object:Gem::Version
|
89
|
-
version: '
|
89
|
+
version: '3'
|
90
90
|
type: :development
|
91
91
|
prerelease: false
|
92
92
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version_requirements: !ruby/object:Gem::Requirement
|
93
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|
requirements:
|
94
|
-
- -
|
94
|
+
- - "~>"
|
95
95
|
- !ruby/object:Gem::Version
|
96
|
-
version: '
|
96
|
+
version: '3'
|
97
97
|
description: Microbial Genomes Atlas
|
98
98
|
email: lmrodriguezr@gmail.com
|
99
99
|
executables:
|
@@ -102,7 +102,25 @@ extensions: []
|
|
102
102
|
extra_rdoc_files:
|
103
103
|
- README.md
|
104
104
|
files:
|
105
|
+
- Gemfile
|
106
|
+
- LICENSE
|
107
|
+
- README.md
|
108
|
+
- Rakefile
|
109
|
+
- actions/add_result
|
110
|
+
- actions/add_taxonomy
|
111
|
+
- actions/create_dataset
|
112
|
+
- actions/create_project
|
113
|
+
- actions/daemon
|
114
|
+
- actions/download_dataset
|
115
|
+
- actions/find_datasets
|
116
|
+
- actions/import_datasets
|
117
|
+
- actions/index_taxonomy
|
118
|
+
- actions/list_datasets
|
119
|
+
- actions/list_files
|
120
|
+
- actions/unlink_dataset
|
121
|
+
- bin/miga
|
105
122
|
- lib/miga.rb
|
123
|
+
- lib/miga/common.rb
|
106
124
|
- lib/miga/daemon.rb
|
107
125
|
- lib/miga/dataset.rb
|
108
126
|
- lib/miga/gui.rb
|
@@ -112,6 +130,7 @@ files:
|
|
112
130
|
- lib/miga/result.rb
|
113
131
|
- lib/miga/tax_index.rb
|
114
132
|
- lib/miga/taxonomy.rb
|
133
|
+
- lib/miga/version.rb
|
115
134
|
- scripts/_distances_noref_nomulti.bash
|
116
135
|
- scripts/_distances_ref_nomulti.bash
|
117
136
|
- scripts/aai_distances.bash
|
@@ -132,53 +151,49 @@ files:
|
|
132
151
|
- scripts/subclades.bash
|
133
152
|
- scripts/trimmed_fasta.bash
|
134
153
|
- scripts/trimmed_reads.bash
|
154
|
+
- test/common_test.rb
|
155
|
+
- test/daemon_test.rb
|
156
|
+
- test/dataset_test.rb
|
157
|
+
- test/jruby_gui_test.rb
|
158
|
+
- test/metadata_test.rb
|
159
|
+
- test/project_test.rb
|
160
|
+
- test/remote_dataset_test.rb
|
161
|
+
- test/tax_index_test.rb
|
162
|
+
- test/taxonomy_test.rb
|
163
|
+
- test/test_helper.rb
|
135
164
|
- utils/adapters.fa
|
136
165
|
- utils/mytaxa_scan.R
|
137
166
|
- utils/mytaxa_scan.rb
|
138
167
|
- utils/requirements.txt
|
139
168
|
- utils/subclades-compile.rb
|
140
169
|
- utils/subclades.R
|
141
|
-
- bin/miga
|
142
|
-
- actions/add_result
|
143
|
-
- actions/add_taxonomy
|
144
|
-
- actions/create_dataset
|
145
|
-
- actions/create_project
|
146
|
-
- actions/daemon
|
147
|
-
- actions/download_dataset
|
148
|
-
- actions/find_datasets
|
149
|
-
- actions/import_datasets
|
150
|
-
- actions/index_taxonomy
|
151
|
-
- actions/list_datasets
|
152
|
-
- actions/list_files
|
153
|
-
- actions/unlink_dataset
|
154
|
-
- README.md
|
155
170
|
homepage: http://enve-omics.ce.gatech.edu/miga
|
156
171
|
licenses:
|
157
|
-
-
|
172
|
+
- Artistic-2.0
|
158
173
|
metadata: {}
|
159
174
|
post_install_message:
|
160
175
|
rdoc_options:
|
161
176
|
- lib
|
162
177
|
- README.md
|
163
|
-
- --main
|
178
|
+
- "--main"
|
164
179
|
- README.md
|
165
|
-
- --title
|
180
|
+
- "--title"
|
166
181
|
- MiGA
|
167
182
|
require_paths:
|
168
183
|
- lib
|
169
184
|
required_ruby_version: !ruby/object:Gem::Requirement
|
170
185
|
requirements:
|
171
|
-
- - ~>
|
186
|
+
- - "~>"
|
172
187
|
- !ruby/object:Gem::Version
|
173
188
|
version: '2.0'
|
174
189
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
175
190
|
requirements:
|
176
|
-
- -
|
191
|
+
- - ">="
|
177
192
|
- !ruby/object:Gem::Version
|
178
193
|
version: '0'
|
179
194
|
requirements: []
|
180
195
|
rubyforge_project:
|
181
|
-
rubygems_version: 2.
|
196
|
+
rubygems_version: 2.5.1
|
182
197
|
signing_key:
|
183
198
|
specification_version: 4
|
184
199
|
summary: MiGA
|