miga-base 0.5.2.1 → 0.5.3.0
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/quality_wf.rb +0 -1
- data/lib/miga/cli/action/wf.rb +22 -14
- data/lib/miga/cli/base.rb +1 -1
- data/lib/miga/version.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: d51a2778df35e38e9396c342db79907aa8b63019e33d62f08a745664c01fc14b
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4
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+
data.tar.gz: 2e553ce8b5fc59aee8aa74f5262d34175c19bbf52c41efa6817353e8e20dbff5
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 0c2ebed3117669c8dce789d731dd478a9eaf8dd8ca9a14e89cf1692908264bca6541073407f7d922a3f72e1edd47d5128275a391b5acc798687edb6302d0b66d
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7
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+
data.tar.gz: 64f0d0fc5af1bca2a3d2fb3ad3a79fdb31a91c95ef346e2cd2b89cc4342a0189ee7a814adae6b7cf5b80b5ce4a80e99cd1196c71afe1138f769fd0f0d91cf3d7
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@@ -25,7 +25,6 @@ class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
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25
25
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%w[project_stats haai_distances aai_distances ani_distances clade_finding]
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26
26
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.map { |i| ["run_#{i}", false] }
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27
27
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]
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28
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-
p_metadata[:ess_coll] = cli[:ess_coll]
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29
28
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d_metadata = { run_distances: false }
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30
29
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d_metadata[:run_mytaxa_scan] = false unless cli[:mytaxa]
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31
30
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p = create_project(:assembly, p_metadata, d_metadata)
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data/lib/miga/cli/action/wf.rb
CHANGED
@@ -115,16 +115,18 @@ module MiGA::Cli::Action::Wf
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115
115
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call_cli([
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116
116
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'new',
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117
117
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'-P', cli[:outdir],
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118
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-
'-t', cli[:project_type]
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119
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-
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120
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-
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118
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+
'-t', cli[:project_type]
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119
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+
]) unless MiGA::Project.exist? cli[:outdir]
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120
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+
# Define project metadata
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121
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+
p = cli.load_project(:outdir, '-o')
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122
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+
[:haai_p, :aai_p, :ani_p, :ess_coll].each { |i| p_metadata[i] = cli[i] }
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123
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+
transfer_metadata(p, p_metadata)
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121
124
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# Download datasets
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122
125
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call_cli([
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123
126
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'ncbi_get',
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124
127
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'-P', cli[:outdir],
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125
128
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'-T', cli[:ncbi_taxon],
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126
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-
(cli[:ncbi_draft] ? '--all' : '--complete')
|
127
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-
'-m', d_metadata.map{ |k,v| "#{k}=#{v}" }.join(',')
|
129
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+
(cli[:ncbi_draft] ? '--all' : '--complete')
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128
130
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]) unless cli[:ncbi_taxon].nil?
|
129
131
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# Add datasets
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130
132
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call_cli([
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@@ -132,15 +134,11 @@ module MiGA::Cli::Action::Wf
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132
134
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'-P', cli[:outdir],
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133
135
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'-t', cli[:dataset_type],
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134
136
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'-i', stage,
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135
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-
'-R', cli[:regexp]
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136
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-
'-m', d_metadata.map{ |k,v| "#{k}=#{v}" }.join(',')
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137
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+
'-R', cli[:regexp]
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137
138
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] + cli.files) unless cli.files.empty?
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138
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-
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139
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-
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140
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-
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141
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-
p.metadata[i] = cli[i] unless cli[i].nil?
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142
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-
end
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143
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-
p.save
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139
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+
# Define datasets metadata
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140
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+
p.load
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141
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+
p.each_dataset { |d| transfer_metadata(d, d_metadata) }
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144
142
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p
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145
143
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end
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146
144
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@@ -159,7 +157,7 @@ module MiGA::Cli::Action::Wf
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159
157
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|
160
158
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def cleanup
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161
159
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return unless cli[:clean]
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162
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-
cli.say
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160
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+
cli.say 'Cleaning up intermediate files'
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163
161
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%w[data daemon metadata miga.project.json].each do |f|
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164
162
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FileUtils.rm_rf(File.expand_path(f, cli[:outdir]))
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165
163
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end
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@@ -180,4 +178,14 @@ module MiGA::Cli::Action::Wf
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180
178
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Dir.chdir(cwd)
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181
179
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end
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182
180
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|
181
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+
def transfer_metadata(obj, md)
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182
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+
# Clear old metadata
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183
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+
obj.metadata.each do |k,v|
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184
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+
obj.metadata[k] = nil if k.to_s =~ /^run_/ || k == :ref_project
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185
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+
end
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186
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+
# Transfer and save
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187
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+
md.each { |k, v| obj.metadata[k] = v }
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188
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+
obj.save
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189
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+
end
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190
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+
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183
191
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end
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data/lib/miga/cli/base.rb
CHANGED
data/lib/miga/version.rb
CHANGED
@@ -10,7 +10,7 @@ module MiGA
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10
10
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# - Float representing the major.minor version.
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11
11
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# - Integer representing gem releases of the current version.
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12
12
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# - Integer representing minor changes that require new version number.
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13
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-
VERSION = [0.5,
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13
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+
VERSION = [0.5, 3, 0]
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14
14
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15
15
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##
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16
16
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# Nickname for the current major.minor version.
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@@ -18,7 +18,7 @@ module MiGA
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18
18
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19
19
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##
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20
20
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# Date of the current gem release.
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21
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-
VERSION_DATE = Date.new(2020, 1,
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21
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+
VERSION_DATE = Date.new(2020, 1, 11)
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22
22
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23
23
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##
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24
24
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# Reference of MiGA.
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metadata
CHANGED
@@ -1,14 +1,14 @@
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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: 0.5.
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4
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+
version: 0.5.3.0
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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: 2020-01-
|
11
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+
date: 2020-01-11 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
|
14
14
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name: daemons
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