lederhosen 2.0.5 → 2.0.6

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Files changed (6) hide show
  1. data/lederhosen.gemspec +3 -2
  2. data/lib/lederhosen/tasks/otu_table.rb +5 -1
  3. data/lib/lederhosen/version.rb +1 -1
  4. data/logo.png +0 -0
  5. data/readme.md +5 -1
  6. metadata +86 -95
data/lederhosen.gemspec CHANGED
@@ -5,11 +5,11 @@
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5
 
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  Gem::Specification.new do |s|
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  s.name = "lederhosen"
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- s.version = "2.0.5"
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+ s.version = "2.0.6"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Austin G. Davis-Richardson"]
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- s.date = "2013-01-27"
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+ s.date = "2013-02-27"
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  s.description = "Various tools for OTU clustering"
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  s.email = "harekrishna@gmail.com"
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  s.executables = ["lederhosen"]
@@ -38,6 +38,7 @@ Gem::Specification.new do |s|
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  "lib/lederhosen/tasks/version.rb",
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  "lib/lederhosen/uc_parser.rb",
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  "lib/lederhosen/version.rb",
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+ "logo.png",
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  "readme.md",
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  "scripts/illumina_pipeline/.gitignore",
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  "scripts/illumina_pipeline/Makefile",
data/lib/lederhosen/tasks/otu_table.rb CHANGED
@@ -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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- parse_taxonomy(taxonomy)[level]
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+ if level == 'original'
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+ taxonomy
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+ else
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+ parse_taxonomy(taxonomy)[level]
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+ end
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  end
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  sample_cluster_count[input_file][tax] += count
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  end
data/lib/lederhosen/version.rb CHANGED
@@ -3,7 +3,7 @@ module Lederhosen
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  MAJOR = 2
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  MINOR = 0
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  CODENAME = 'Schnittlauchbrot' # changes for minor versions
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- PATCH = 5
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+ PATCH = 6
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  STRING = [MAJOR, MINOR, PATCH].join('.')
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  end
data/logo.png ADDED
Binary file
data/readme.md CHANGED
@@ -1,4 +1,4 @@
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- <img src="http://d.pr/i/26Js+#.png" align="right">
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+ <img src="https://raw.github.com/audy/lederhosen/master/logo.png" align="right">
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  # Lederhosen
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4
 
@@ -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.
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+ ### Need Help?
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+
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+ Bug me: [@heyaudy](http://twitter.com/heyaudy) (twitter)
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+
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  ## Tasks
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  Lederhosen is invoked by typing `lederhosen [TASK]`
metadata CHANGED
@@ -1,108 +1,104 @@
1
- --- !ruby/object:Gem::Specification
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+ --- !ruby/object:Gem::Specification
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  name: lederhosen
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- version: !ruby/object:Gem::Version
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- hash: 5
3
+ version: !ruby/object:Gem::Version
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+ version: 2.0.6
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  prerelease:
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- segments:
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- - 2
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- - 0
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- - 5
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- version: 2.0.5
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  platform: ruby
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- authors:
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+ authors:
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  - Austin G. Davis-Richardson
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  autorequire:
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  bindir: bin
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  cert_chain: []
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-
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- date: 2013-01-27 00:00:00 Z
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- dependencies:
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- - !ruby/object:Gem::Dependency
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- prerelease: false
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- requirement: &id001 !ruby/object:Gem::Requirement
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+ date: 2013-02-27 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: dna
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+ requirement: !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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- hash: 3
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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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  type: :runtime
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- name: dna
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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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- requirement: &id002 !ruby/object:Gem::Requirement
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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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- hash: 47
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- segments:
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- - 0
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- - 12
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- - 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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+ - !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:
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+ - - '='
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+ - !ruby/object:Gem::Version
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  version: 0.12.0
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  type: :runtime
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- name: progressbar
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- version_requirements: *id002
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- - !ruby/object:Gem::Dependency
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  prerelease: false
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- requirement: &id003 !ruby/object:Gem::Requirement
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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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- hash: 95
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- segments:
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- - 0
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- - 16
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- - 0
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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
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+ - !ruby/object:Gem::Dependency
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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:
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+ - - '='
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+ - !ruby/object:Gem::Version
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  version: 0.16.0
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  type: :runtime
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- name: thor
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- version_requirements: *id003
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- - !ruby/object:Gem::Dependency
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  prerelease: false
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- requirement: &id004 !ruby/object:Gem::Requirement
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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: 0.16.0
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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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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  - - ~>
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- - !ruby/object:Gem::Version
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- hash: 31
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- segments:
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- - 3
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- - 12
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- version: "3.12"
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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  type: :development
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- name: rdoc
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- version_requirements: *id004
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- - !ruby/object:Gem::Dependency
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  prerelease: false
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- requirement: &id005 !ruby/object:Gem::Requirement
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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: '3.12'
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: !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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- 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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- name: jeweler
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- version_requirements: *id005
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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
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  email: harekrishna@gmail.com
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- executables:
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+ executables:
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  - lederhosen
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  extensions: []
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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
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  - lib/lederhosen/uc_parser.rb
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  - lib/lederhosen/version.rb
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+ - logo.png
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  - readme.md
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  - scripts/illumina_pipeline/.gitignore
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  - scripts/illumina_pipeline/Makefile
@@ -138,37 +135,31 @@ files:
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  - spec/spec_helper.rb
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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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  - 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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  - 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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- hash: 3
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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
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- version: "0"
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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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- hash: 3
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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: []
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-
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  rubyforge_project:
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  rubygems_version: 1.8.24
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  signing_key:
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  specification_version: 3
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  summary: OTU Clustering
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  test_files: []
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-