rput 0.1.0 → 0.1.1
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- data/Gemfile +2 -0
- data/Gemfile.lock +4 -0
- data/VERSION +1 -1
- data/lib/experiment.rb +3 -3
- data/lib/rput.rb +3 -0
- data/lib/starter.rb +3 -4
- data/rput.gemspec +8 -1
- metadata +36 -3
data/Gemfile
CHANGED
data/Gemfile.lock
CHANGED
@@ -12,6 +12,8 @@ GEM
|
|
12
12
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rcov (1.0.0)
|
13
13
|
rdoc (3.12)
|
14
14
|
json (~> 1.4)
|
15
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+
rnewick (0.1.0)
|
16
|
+
rphylip (0.1.0)
|
15
17
|
rraxml (0.1.2)
|
16
18
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shoulda (3.0.1)
|
17
19
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shoulda-context (~> 1.0.0)
|
@@ -27,5 +29,7 @@ DEPENDENCIES
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|
27
29
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jeweler (~> 1.8.3)
|
28
30
|
rcov
|
29
31
|
rdoc (~> 3.12)
|
32
|
+
rnewick (~> 0.1.0)
|
33
|
+
rphylip (~> 0.1.0)
|
30
34
|
rraxml (~> 0.1.2)
|
31
35
|
shoulda
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.1.
|
1
|
+
0.1.1
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data/lib/experiment.rb
CHANGED
@@ -1,12 +1,12 @@
|
|
1
1
|
#!/usr/bin/env ruby
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2
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-
|
2
|
+
require 'rphylip'
|
3
3
|
require 'fileutils'
|
4
4
|
require 'yaml'
|
5
5
|
|
6
6
|
class Experiment
|
7
|
-
def initialize(name)
|
7
|
+
def initialize(name, basedir)
|
8
8
|
@name = name
|
9
|
-
@base_dir =
|
9
|
+
@base_dir = basedir
|
10
10
|
end
|
11
11
|
def dirname(a)
|
12
12
|
File.join @base_dir, 'experiments', @name, a
|
data/lib/rput.rb
ADDED
data/lib/starter.rb
CHANGED
data/rput.gemspec
CHANGED
@@ -5,7 +5,7 @@
|
|
5
5
|
|
6
6
|
Gem::Specification.new do |s|
|
7
7
|
s.name = %q{rput}
|
8
|
-
s.version = "0.1.
|
8
|
+
s.version = "0.1.1"
|
9
9
|
|
10
10
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
11
|
s.authors = [%q{Fernando Izquierdo-Carrasco}]
|
@@ -25,6 +25,7 @@ Gem::Specification.new do |s|
|
|
25
25
|
"Rakefile",
|
26
26
|
"VERSION",
|
27
27
|
"lib/experiment.rb",
|
28
|
+
"lib/rput.rb",
|
28
29
|
"lib/starter.rb",
|
29
30
|
"rput.gemspec",
|
30
31
|
"test/helper.rb",
|
@@ -46,6 +47,8 @@ Gem::Specification.new do |s|
|
|
46
47
|
s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
|
47
48
|
s.add_development_dependency(%q<rcov>, [">= 0"])
|
48
49
|
s.add_development_dependency(%q<rraxml>, ["~> 0.1.2"])
|
50
|
+
s.add_development_dependency(%q<rphylip>, ["~> 0.1.0"])
|
51
|
+
s.add_development_dependency(%q<rnewick>, ["~> 0.1.0"])
|
49
52
|
else
|
50
53
|
s.add_dependency(%q<shoulda>, [">= 0"])
|
51
54
|
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
@@ -53,6 +56,8 @@ Gem::Specification.new do |s|
|
|
53
56
|
s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
|
54
57
|
s.add_dependency(%q<rcov>, [">= 0"])
|
55
58
|
s.add_dependency(%q<rraxml>, ["~> 0.1.2"])
|
59
|
+
s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
|
60
|
+
s.add_dependency(%q<rnewick>, ["~> 0.1.0"])
|
56
61
|
end
|
57
62
|
else
|
58
63
|
s.add_dependency(%q<shoulda>, [">= 0"])
|
@@ -61,6 +66,8 @@ Gem::Specification.new do |s|
|
|
61
66
|
s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
|
62
67
|
s.add_dependency(%q<rcov>, [">= 0"])
|
63
68
|
s.add_dependency(%q<rraxml>, ["~> 0.1.2"])
|
69
|
+
s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
|
70
|
+
s.add_dependency(%q<rnewick>, ["~> 0.1.0"])
|
64
71
|
end
|
65
72
|
end
|
66
73
|
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rput
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 25
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 1
|
9
|
-
-
|
10
|
-
version: 0.1.
|
9
|
+
- 1
|
10
|
+
version: 0.1.1
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Fernando Izquierdo-Carrasco
|
@@ -108,6 +108,38 @@ dependencies:
|
|
108
108
|
version_requirements: *id006
|
109
109
|
name: rraxml
|
110
110
|
prerelease: false
|
111
|
+
- !ruby/object:Gem::Dependency
|
112
|
+
type: :development
|
113
|
+
requirement: &id007 !ruby/object:Gem::Requirement
|
114
|
+
none: false
|
115
|
+
requirements:
|
116
|
+
- - ~>
|
117
|
+
- !ruby/object:Gem::Version
|
118
|
+
hash: 27
|
119
|
+
segments:
|
120
|
+
- 0
|
121
|
+
- 1
|
122
|
+
- 0
|
123
|
+
version: 0.1.0
|
124
|
+
version_requirements: *id007
|
125
|
+
name: rphylip
|
126
|
+
prerelease: false
|
127
|
+
- !ruby/object:Gem::Dependency
|
128
|
+
type: :development
|
129
|
+
requirement: &id008 !ruby/object:Gem::Requirement
|
130
|
+
none: false
|
131
|
+
requirements:
|
132
|
+
- - ~>
|
133
|
+
- !ruby/object:Gem::Version
|
134
|
+
hash: 27
|
135
|
+
segments:
|
136
|
+
- 0
|
137
|
+
- 1
|
138
|
+
- 0
|
139
|
+
version: 0.1.0
|
140
|
+
version_requirements: *id008
|
141
|
+
name: rnewick
|
142
|
+
prerelease: false
|
111
143
|
description: Automated iterations of raxml runs over externally-extended phylip files
|
112
144
|
email: fer.izquierdo@gmail.com
|
113
145
|
executables: []
|
@@ -126,6 +158,7 @@ files:
|
|
126
158
|
- Rakefile
|
127
159
|
- VERSION
|
128
160
|
- lib/experiment.rb
|
161
|
+
- lib/rput.rb
|
129
162
|
- lib/starter.rb
|
130
163
|
- rput.gemspec
|
131
164
|
- test/helper.rb
|