lederhosen 2.0.5 → 2.0.6
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- data/lederhosen.gemspec +3 -2
- data/lib/lederhosen/tasks/otu_table.rb +5 -1
- data/lib/lederhosen/version.rb +1 -1
- data/logo.png +0 -0
- data/readme.md +5 -1
- metadata +86 -95
data/lederhosen.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
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7
7
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s.name = "lederhosen"
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8
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-
s.version = "2.0.
|
8
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+
s.version = "2.0.6"
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9
9
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10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["Austin G. Davis-Richardson"]
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12
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-
s.date = "2013-
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12
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+
s.date = "2013-02-27"
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13
13
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s.description = "Various tools for OTU clustering"
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14
14
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s.email = "harekrishna@gmail.com"
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15
15
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s.executables = ["lederhosen"]
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@@ -38,6 +38,7 @@ Gem::Specification.new do |s|
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38
38
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"lib/lederhosen/tasks/version.rb",
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39
39
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"lib/lederhosen/uc_parser.rb",
|
40
40
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"lib/lederhosen/version.rb",
|
41
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+
"logo.png",
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41
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"readme.md",
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43
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"scripts/illumina_pipeline/.gitignore",
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"scripts/illumina_pipeline/Makefile",
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@@ -39,7 +39,11 @@ module Lederhosen
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if taxonomy == 'unclassified_reads'
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'unclassified_reads'
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else
|
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-
|
42
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+
if level == 'original'
|
43
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+
taxonomy
|
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+
else
|
45
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+
parse_taxonomy(taxonomy)[level]
|
46
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+
end
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43
47
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end
|
44
48
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sample_cluster_count[input_file][tax] += count
|
45
49
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end
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data/lib/lederhosen/version.rb
CHANGED
data/logo.png
ADDED
Binary file
|
data/readme.md
CHANGED
@@ -1,4 +1,4 @@
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1
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-
<img src="
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1
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+
<img src="https://raw.github.com/audy/lederhosen/master/logo.png" align="right">
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2
2
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3
3
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# Lederhosen
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4
4
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@@ -51,6 +51,10 @@ using paired and non-paired end short reads such as those produced by Illumina (
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`sudo gem install lederhosen`
|
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4. Check installation by typing `lederhosen`. You should see some help text.
|
53
53
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|
54
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+
### Need Help?
|
55
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+
|
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+
Bug me: [@heyaudy](http://twitter.com/heyaudy) (twitter)
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+
|
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58
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## Tasks
|
55
59
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|
56
60
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Lederhosen is invoked by typing `lederhosen [TASK]`
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metadata
CHANGED
@@ -1,108 +1,104 @@
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1
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-
--- !ruby/object:Gem::Specification
|
1
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+
--- !ruby/object:Gem::Specification
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2
2
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name: lederhosen
|
3
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-
version: !ruby/object:Gem::Version
|
4
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-
|
3
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+
version: !ruby/object:Gem::Version
|
4
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+
version: 2.0.6
|
5
5
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prerelease:
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6
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-
segments:
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7
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-
- 2
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8
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-
- 0
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9
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-
- 5
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10
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-
version: 2.0.5
|
11
6
|
platform: ruby
|
12
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-
authors:
|
7
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+
authors:
|
13
8
|
- Austin G. Davis-Richardson
|
14
9
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autorequire:
|
15
10
|
bindir: bin
|
16
11
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cert_chain: []
|
17
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-
|
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-
|
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-
|
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-
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-
|
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-
requirement: &id001 !ruby/object:Gem::Requirement
|
12
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+
date: 2013-02-27 00:00:00.000000000 Z
|
13
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+
dependencies:
|
14
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+
- !ruby/object:Gem::Dependency
|
15
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+
name: dna
|
16
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+
requirement: !ruby/object:Gem::Requirement
|
23
17
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none: false
|
24
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-
requirements:
|
25
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-
- -
|
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-
- !ruby/object:Gem::Version
|
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-
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-
segments:
|
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-
- 0
|
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-
version: "0"
|
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+
requirements:
|
19
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+
- - ! '>='
|
20
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+
- !ruby/object:Gem::Version
|
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+
version: '0'
|
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type: :runtime
|
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-
name: dna
|
33
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-
version_requirements: *id001
|
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-
- !ruby/object:Gem::Dependency
|
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prerelease: false
|
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-
|
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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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-
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-
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-
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-
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+
requirements:
|
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+
- - ! '>='
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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: progressbar
|
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+
requirement: !ruby/object:Gem::Requirement
|
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+
none: false
|
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+
requirements:
|
35
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+
- - '='
|
36
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+
- !ruby/object:Gem::Version
|
46
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version: 0.12.0
|
47
38
|
type: :runtime
|
48
|
-
name: progressbar
|
49
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-
version_requirements: *id002
|
50
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-
- !ruby/object:Gem::Dependency
|
51
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prerelease: false
|
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-
|
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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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-
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-
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-
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-
|
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+
requirements:
|
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+
- - '='
|
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+
- !ruby/object:Gem::Version
|
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+
version: 0.12.0
|
46
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+
- !ruby/object:Gem::Dependency
|
47
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+
name: thor
|
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+
requirement: !ruby/object:Gem::Requirement
|
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+
none: false
|
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+
requirements:
|
51
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+
- - '='
|
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+
- !ruby/object:Gem::Version
|
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version: 0.16.0
|
63
54
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type: :runtime
|
64
|
-
name: thor
|
65
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-
version_requirements: *id003
|
66
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-
- !ruby/object:Gem::Dependency
|
67
55
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prerelease: false
|
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|
-
|
56
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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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+
- - '='
|
60
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+
- !ruby/object:Gem::Version
|
61
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+
version: 0.16.0
|
62
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+
- !ruby/object:Gem::Dependency
|
63
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+
name: rdoc
|
64
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+
requirement: !ruby/object:Gem::Requirement
|
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none: false
|
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-
requirements:
|
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+
requirements:
|
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67
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- - ~>
|
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-
- !ruby/object:Gem::Version
|
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-
|
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-
segments:
|
75
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-
- 3
|
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-
- 12
|
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-
version: "3.12"
|
68
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+
- !ruby/object:Gem::Version
|
69
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+
version: '3.12'
|
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70
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type: :development
|
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-
name: rdoc
|
80
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-
version_requirements: *id004
|
81
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-
- !ruby/object:Gem::Dependency
|
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prerelease: false
|
83
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-
|
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
|
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+
requirements:
|
75
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+
- - ~>
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76
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+
- !ruby/object:Gem::Version
|
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+
version: '3.12'
|
78
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+
- !ruby/object:Gem::Dependency
|
79
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+
name: jeweler
|
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+
requirement: !ruby/object:Gem::Requirement
|
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none: false
|
85
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-
requirements:
|
86
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-
- -
|
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-
- !ruby/object:Gem::Version
|
88
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-
hash: 63
|
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-
segments:
|
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-
- 1
|
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-
- 8
|
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-
- 4
|
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+
requirements:
|
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+
- - '='
|
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+
- !ruby/object:Gem::Version
|
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version: 1.8.4
|
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type: :development
|
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-
|
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-
version_requirements:
|
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+
prerelease: false
|
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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: 1.8.4
|
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description: Various tools for OTU clustering
|
98
95
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email: harekrishna@gmail.com
|
99
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-
executables:
|
96
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+
executables:
|
100
97
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- lederhosen
|
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98
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extensions: []
|
102
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-
|
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-
extra_rdoc_files:
|
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+
extra_rdoc_files:
|
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- LICENSE.txt
|
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-
files:
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+
files:
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- .rspec
|
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- Gemfile
|
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- LICENSE.txt
|
@@ -124,6 +120,7 @@ files:
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- lib/lederhosen/tasks/version.rb
|
125
121
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- lib/lederhosen/uc_parser.rb
|
126
122
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- lib/lederhosen/version.rb
|
123
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+
- logo.png
|
127
124
|
- readme.md
|
128
125
|
- scripts/illumina_pipeline/.gitignore
|
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126
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- scripts/illumina_pipeline/Makefile
|
@@ -138,37 +135,31 @@ files:
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- spec/spec_helper.rb
|
139
136
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- spec/uc_parser_spec.rb
|
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homepage: http://audy.github.com/lederhosen
|
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-
licenses:
|
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+
licenses:
|
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139
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- MIT
|
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post_install_message:
|
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rdoc_options: []
|
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-
|
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-
require_paths:
|
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+
require_paths:
|
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143
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- lib
|
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-
required_ruby_version: !ruby/object:Gem::Requirement
|
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+
required_ruby_version: !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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segments:
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requirements:
|
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+
- - ! '>='
|
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- !ruby/object:Gem::Version
|
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version: '0'
|
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+
segments:
|
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- 0
|
156
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-
|
157
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-
required_rubygems_version: !ruby/object:Gem::Requirement
|
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+
hash: -902984509893215788
|
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+
required_rubygems_version: !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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-
segments:
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-
- 0
|
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version: "0"
|
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requirements:
|
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- - ! '>='
|
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+
- !ruby/object:Gem::Version
|
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+
version: '0'
|
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requirements: []
|
167
|
-
|
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rubyforge_project:
|
169
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rubygems_version: 1.8.24
|
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|
signing_key:
|
171
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specification_version: 3
|
172
164
|
summary: OTU Clustering
|
173
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|
test_files: []
|
174
|
-
|