lederhosen 3.2.0 → 3.2.1
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- checksums.yaml +7 -0
- data/.travis.yml +2 -1
- data/Gemfile +6 -6
- data/lederhosen.gemspec +9 -8
- data/lib/lederhosen.rb +5 -1
- data/lib/lederhosen/version.rb +1 -1
- data/readme.md +3 -3
- data/spec/no_tasks_spec.rb +1 -1
- data/spec/spec_helper.rb +2 -0
- metadata +19 -34
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
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1
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+
---
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SHA1:
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metadata.gz: d4f049c98435fbc48c6b5d7f399346d05c5f0847
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data.tar.gz: 048cc246fd1eee492f9d74179622197451f8496a
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SHA512:
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metadata.gz: 7d3faf78771049bafbfd3227391dd1729001cf18e6f9eab358ef058c9f52cee7cf78722c5250f54bc22d804deaf4446b4e56402af737f9a1603a8e4c624cba4f
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7
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+
data.tar.gz: 72740fa34f9eb725616c548cf68ba42ebcb0284e6c023ed4c5bb70151841ae3ecc311c09fdaba87d70ac849d8ddcfc3d4da8a548d6aeb4f4a990d90cdba75680
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data/.travis.yml
CHANGED
data/Gemfile
CHANGED
@@ -4,12 +4,12 @@ gem 'dna', '0.3.0'
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4
4
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gem 'progressbar', '0.12.0'
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5
5
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gem 'thor', '0.16.0'
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6
6
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7
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-
group :test do
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8
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-
gem 'rspec', '2.12.0'
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9
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-
gem 'pry'
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10
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-
end
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11
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-
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12
7
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group :development do
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-
gem 'rdoc', '~> 3.12'
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14
8
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gem 'jeweler', '1.8.4'
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9
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+
gem 'rdoc', '~> 3.12'
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10
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+
end
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11
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+
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group :test do
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gem 'pry'
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gem 'rspec', '2.12.0'
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end
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data/lederhosen.gemspec
CHANGED
@@ -2,14 +2,16 @@
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2
2
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# DO NOT EDIT THIS FILE DIRECTLY
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3
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: lederhosen 3.2.1 ruby lib
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6
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Gem::Specification.new do |s|
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s.name = "lederhosen"
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8
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-
s.version = "3.2.
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9
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+
s.version = "3.2.1"
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9
10
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10
11
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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12
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+
s.require_paths = ["lib"]
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11
13
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s.authors = ["Austin G. Davis-Richardson"]
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12
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-
s.date = "
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14
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+
s.date = "2014-04-16"
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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"]
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@@ -57,32 +59,31 @@ Gem::Specification.new do |s|
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57
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]
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s.homepage = "http://audy.github.com/lederhosen"
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59
61
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s.licenses = ["MIT"]
|
60
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-
s.
|
61
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-
s.rubygems_version = "1.8.25"
|
62
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+
s.rubygems_version = "2.2.2"
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62
63
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s.summary = "OTU Clustering"
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63
64
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|
64
65
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if s.respond_to? :specification_version then
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65
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-
s.specification_version =
|
66
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+
s.specification_version = 4
|
66
67
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|
67
68
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
68
69
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s.add_runtime_dependency(%q<dna>, ["= 0.3.0"])
|
69
70
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s.add_runtime_dependency(%q<progressbar>, ["= 0.12.0"])
|
70
71
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s.add_runtime_dependency(%q<thor>, ["= 0.16.0"])
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71
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-
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
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72
72
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s.add_development_dependency(%q<jeweler>, ["= 1.8.4"])
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+
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
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else
|
74
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s.add_dependency(%q<dna>, ["= 0.3.0"])
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s.add_dependency(%q<progressbar>, ["= 0.12.0"])
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76
77
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s.add_dependency(%q<thor>, ["= 0.16.0"])
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77
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-
s.add_dependency(%q<rdoc>, ["~> 3.12"])
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78
78
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s.add_dependency(%q<jeweler>, ["= 1.8.4"])
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+
s.add_dependency(%q<rdoc>, ["~> 3.12"])
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end
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else
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81
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s.add_dependency(%q<dna>, ["= 0.3.0"])
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s.add_dependency(%q<progressbar>, ["= 0.12.0"])
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83
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s.add_dependency(%q<thor>, ["= 0.16.0"])
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84
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-
s.add_dependency(%q<rdoc>, ["~> 3.12"])
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85
85
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s.add_dependency(%q<jeweler>, ["= 1.8.4"])
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86
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+
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
86
87
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end
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87
88
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end
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data/lib/lederhosen.rb
CHANGED
@@ -3,4 +3,8 @@ require 'dna'
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3
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require 'progressbar'
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require 'thor'
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-
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6
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# files have to be required in order.
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7
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# changes depending on system.
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8
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%w{cli no_tasks uc_parser version}.each do |f|
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9
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require File.join(File.dirname(__FILE__), 'lederhosen', "#{f}.rb")
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end
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data/lib/lederhosen/version.rb
CHANGED
data/readme.md
CHANGED
@@ -29,7 +29,7 @@ the USEARCH license, Lederhosen is free for commercial use.
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Tested using Ruby 1.9.3 and 2.0.0 (1.8.7 not supported)
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-
0. Obtain & Install [USEARCH](http://www.drive5.com/).
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+
0. Obtain & Install [USEARCH](http://www.drive5.com/) version 7.
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1. Get a database:
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- [TaxCollector](http://github.com/audy/taxcollector)
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- [GreenGenes 13.5 Rep. Set](http://greengenes.secondgenome.com/downloads) 16S
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@@ -90,11 +90,11 @@ do
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echo lederhosen cluster \
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--input=$reads_file \
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--identity=0.95 \
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-
--output=$(basename $
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--output=$(basename $reads_file .fasta).95.uc \
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--database=taxcollector.udb \
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--threads 1 \
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--dry-run
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-
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+
done > jobs.sh
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# send jobs to queue system
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cat jobs.sh | parallel -j 24 # run 24 parallel jobs
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data/spec/no_tasks_spec.rb
CHANGED
@@ -1,6 +1,6 @@
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1
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require 'spec_helper'
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-
describe 'no_tasks' do
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describe 'Lederhosen::CLI.no_tasks' do
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let(:greengenes_taxonomies) { ['124 U55236.1 Methanobrevibacter thaueri str. CW k__domain; p__phylum; c__class; o__order; f__family; g__genus; species; otu_127']}
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let(:greengenes135_taxonomies) { ['k__domain; p__phylum; c__class; o__order; f__family; g__genus; s__species']}
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data/spec/spec_helper.rb
CHANGED
metadata
CHANGED
@@ -1,20 +1,18 @@
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1
1
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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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version: 3.2.
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prerelease:
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version: 3.2.1
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platform: ruby
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6
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authors:
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8
7
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- Austin G. Davis-Richardson
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8
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autorequire:
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9
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bindir: bin
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cert_chain: []
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-
date:
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date: 2014-04-16 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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18
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- !ruby/object:Gem::Version
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@@ -22,7 +20,6 @@ dependencies:
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type: :runtime
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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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@@ -30,7 +27,6 @@ dependencies:
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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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@@ -38,7 +34,6 @@ dependencies:
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type: :runtime
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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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@@ -46,7 +41,6 @@ dependencies:
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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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@@ -54,43 +48,38 @@ dependencies:
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type: :runtime
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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: 0.16.0
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- !ruby/object:Gem::Dependency
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-
name:
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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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+
- - '='
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- !ruby/object:Gem::Version
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-
version:
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version: 1.8.4
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type: :development
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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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+
- - '='
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- !ruby/object:Gem::Version
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version:
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version: 1.8.4
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- !ruby/object:Gem::Dependency
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name:
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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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-
- -
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+
- - "~>"
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- !ruby/object:Gem::Version
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version:
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version: '3.12'
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type: :development
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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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+
- - "~>"
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- !ruby/object:Gem::Version
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-
version:
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version: '3.12'
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description: Various tools for OTU clustering
|
95
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email: harekrishna@gmail.com
|
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executables:
|
@@ -99,8 +88,8 @@ extensions: []
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extra_rdoc_files:
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- LICENSE.txt
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files:
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-
- .rspec
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-
- .travis.yml
|
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+
- ".rspec"
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- ".travis.yml"
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- Gemfile
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- LICENSE.txt
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- Rakefile
|
@@ -139,29 +128,25 @@ files:
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139
128
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homepage: http://audy.github.com/lederhosen
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licenses:
|
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- MIT
|
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+
metadata: {}
|
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post_install_message:
|
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rdoc_options: []
|
144
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require_paths:
|
145
135
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- lib
|
146
136
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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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+
- - ">="
|
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139
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- !ruby/object:Gem::Version
|
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140
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version: '0'
|
152
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-
segments:
|
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-
- 0
|
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-
hash: -502231150747974462
|
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required_rubygems_version: !ruby/object:Gem::Requirement
|
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-
none: false
|
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142
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requirements:
|
158
|
-
- -
|
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+
- - ">="
|
159
144
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- !ruby/object:Gem::Version
|
160
145
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version: '0'
|
161
146
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requirements: []
|
162
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|
rubyforge_project:
|
163
|
-
rubygems_version:
|
148
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+
rubygems_version: 2.2.2
|
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signing_key:
|
165
|
-
specification_version:
|
150
|
+
specification_version: 4
|
166
151
|
summary: OTU Clustering
|
167
152
|
test_files: []
|