lederhosen 0.2.7 → 0.2.8
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- data/Gemfile +11 -1
- data/Rakefile +56 -0
- data/lib/lederhosen/version.rb +9 -0
- data/spec/{pipeline_spec.rb → cli_spec.rb} +9 -3
- metadata +82 -36
- data/.gitignore +0 -1
- data/lederhosen.gemspec +0 -24
- data/lib/version.rb +0 -3
- /data/{examples → pipelines}/hierarchical_clustering.sh +0 -0
- /data/{examples → pipelines}/pipeline.sh +0 -0
data/Gemfile
CHANGED
data/Rakefile
ADDED
@@ -0,0 +1,56 @@
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1
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+
# encoding: utf-8
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+
require 'rubygems'
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4
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require 'bundler'
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5
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+
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6
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+
require './lib/lederhosen/version.rb'
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7
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+
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8
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+
begin
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9
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Bundler.setup(:default, :development)
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10
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rescue Bundler::BundlerError => e
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11
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$stderr.puts e.message
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12
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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14
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end
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15
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require 'rake'
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16
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+
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17
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require 'jeweler'
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18
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Jeweler::Tasks.new do |gem|
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19
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gem.name = "lederhosen"
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20
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gem.homepage = "http://github.com/audy/lederhosen"
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gem.license = "MIT"
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gem.summary = "OTU Clustering"
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gem.description = "Various tools for OTU clustering"
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gem.email = "harekrishna@gmail.com"
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25
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gem.authors = ["Austin G. Davis-Richardson"]
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26
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gem.version = Lederhosen::Version::STRING
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end
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28
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Jeweler::RubygemsDotOrgTasks.new
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29
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require 'rake/testtask'
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31
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Rake::TestTask.new(:test) do |test|
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32
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test.libs << 'lib' << 'test'
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33
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test.pattern = 'test/**/test_*.rb'
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34
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test.verbose = true
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35
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end
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36
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37
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require 'rcov/rcovtask'
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38
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Rcov::RcovTask.new do |test|
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39
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test.libs << 'test'
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40
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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42
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test.rcov_opts << '--exclude "gems/*"'
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end
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45
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task :default => :test
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require 'rdoc/task'
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48
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Rake::RDocTask.new do |rdoc|
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50
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version = Lederhosen::Version::STRING
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51
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+
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52
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rdoc.rdoc_dir = 'rdoc'
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53
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rdoc.title = "test #{version}"
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54
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rdoc.rdoc_files.include('readme.md')
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55
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rdoc.rdoc_files.include('lib/**/*.rb')
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56
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end
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@@ -1,8 +1,8 @@
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require 'spec_helper'
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2
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describe
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describe Lederhosen::CLI do
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it 'should
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5
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it 'should have an executable' do
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`./bin/lederhosen`
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$?.success?.should be_true
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8
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end
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@@ -41,7 +41,13 @@ describe 'the pipeline' do
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`./bin/lederhosen split --reads=#{$test_dir}/joined.fasta --clusters=#{$test_dir}/clusters.uc --out-dir=#{$test_dir}/split --min-clst-size=1`
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42
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end
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44
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it 'should
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44
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it 'should create a fasta file containing representative reads for each cluster' do
|
45
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`./bin/lederhosen rep_reads --clusters=#{$test_dir}/clusters.uc --joined=#{$test_dir}/filtered.fasta --output=#{$test_dir}/representatives.fasta`
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$?.success?.should be_true
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end
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48
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+
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49
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# Need a taxcollector database for this one.
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it 'should identify clusters given a taxcollector database'
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it 'should add names to otu abundance matrix given blat output' do
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level = %w{kingdom domain phylum class order genus speces}.choice
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metadata
CHANGED
@@ -1,13 +1,13 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: lederhosen
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version: !ruby/object:Gem::Version
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4
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-
hash:
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4
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+
hash: 7
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5
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prerelease:
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segments:
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7
7
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- 0
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8
8
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- 2
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9
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-
-
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10
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-
version: 0.2.
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9
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- 8
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version: 0.2.8
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platform: ruby
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authors:
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- Austin G. Davis-Richardson
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@@ -15,11 +15,10 @@ autorequire:
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bindir: bin
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cert_chain: []
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18
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-
date: 2012-08-
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+
date: 2012-08-07 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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-
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-
prerelease: false
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+
type: :runtime
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requirement: &id001 !ruby/object:Gem::Requirement
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none: false
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requirements:
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@@ -29,11 +28,11 @@ dependencies:
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segments:
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- 0
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version: "0"
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type: :runtime
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version_requirements: *id001
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-
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name: thor
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32
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name: dna
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prerelease: false
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- !ruby/object:Gem::Dependency
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type: :runtime
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requirement: &id002 !ruby/object:Gem::Requirement
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none: false
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requirements:
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@@ -43,11 +42,11 @@ dependencies:
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segments:
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- 0
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version: "0"
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type: :runtime
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version_requirements: *id002
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48
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-
- !ruby/object:Gem::Dependency
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name: progressbar
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prerelease: false
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48
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- !ruby/object:Gem::Dependency
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type: :runtime
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requirement: &id003 !ruby/object:Gem::Requirement
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none: false
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requirements:
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@@ -57,11 +56,68 @@ dependencies:
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segments:
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- 0
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version: "0"
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type: :runtime
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version_requirements: *id003
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-
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-
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-
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name: thor
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prerelease: false
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- !ruby/object:Gem::Dependency
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type: :development
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64
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requirement: &id004 !ruby/object:Gem::Requirement
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65
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none: false
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66
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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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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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version_requirements: *id004
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name: rdoc
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prerelease: false
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77
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- !ruby/object:Gem::Dependency
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type: :development
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requirement: &id005 !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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version_requirements: *id005
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89
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name: bundler
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prerelease: false
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91
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- !ruby/object:Gem::Dependency
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type: :development
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requirement: &id006 !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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version_requirements: *id006
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name: jeweler
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prerelease: false
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- !ruby/object:Gem::Dependency
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type: :development
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requirement: &id007 !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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version_requirements: *id007
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name: rcov
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prerelease: false
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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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- lederhosen
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extensions: []
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@@ -69,14 +125,11 @@ extensions: []
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extra_rdoc_files: []
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files:
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-
- .gitignore
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- .rspec
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- .rvmrc
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- Gemfile
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- Rakefile
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- bin/lederhosen
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-
- examples/hierarchical_clustering.sh
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- examples/pipeline.sh
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79
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- lederhosen.gemspec
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133
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- lib/lederhosen.rb
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81
134
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- lib/lederhosen/buffer.rb
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- lib/lederhosen/cli.rb
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@@ -96,8 +149,11 @@ files:
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149
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- lib/lederhosen/tasks/uc_filter.rb
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- lib/lederhosen/tasks/uc_stats.rb
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151
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- lib/lederhosen/tasks/uniquify.rb
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99
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-
- lib/version.rb
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152
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+
- lib/lederhosen/version.rb
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- pipelines/hierarchical_clustering.sh
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- pipelines/pipeline.sh
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- readme.md
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- spec/cli_spec.rb
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157
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- spec/data/ILT_L_9_B_001_1.txt.gz
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- spec/data/ILT_L_9_B_001_3.txt.gz
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- spec/data/ILT_L_9_B_002_1.txt.gz
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@@ -106,11 +162,10 @@ files:
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- spec/data/otus.csv
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107
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- spec/helpers_spec.rb
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- spec/misc_spec.rb
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109
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-
- spec/pipeline_spec.rb
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- spec/spec_helper.rb
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homepage: http://github.com/audy/lederhosen
|
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licenses:
|
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-
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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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@@ -136,19 +191,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: "0"
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137
192
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requirements: []
|
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|
139
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-
rubyforge_project:
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+
rubyforge_project:
|
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rubygems_version: 1.8.24
|
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196
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signing_key:
|
142
197
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specification_version: 3
|
143
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-
summary:
|
144
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-
test_files:
|
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-
|
146
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-
- spec/data/ILT_L_9_B_001_3.txt.gz
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147
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- spec/data/ILT_L_9_B_002_1.txt.gz
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-
- spec/data/ILT_L_9_B_002_3.txt.gz
|
149
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-
- spec/data/blat.txt
|
150
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-
- spec/data/otus.csv
|
151
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-
- spec/helpers_spec.rb
|
152
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- spec/misc_spec.rb
|
153
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-
- spec/pipeline_spec.rb
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154
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-
- spec/spec_helper.rb
|
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summary: OTU Clustering
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199
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test_files: []
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200
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+
|
data/.gitignore
DELETED
@@ -1 +0,0 @@
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1
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-
*.swp
|
data/lederhosen.gemspec
DELETED
@@ -1,24 +0,0 @@
|
|
1
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-
# -*- encoding: utf-8 -*-
|
2
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-
|
3
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-
require File.join(File.dirname(__FILE__), 'lib/version')
|
4
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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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7
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s.version = Lederhosen::VERSION
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8
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s.authors = ["Austin G. Davis-Richardson"]
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9
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s.email = ["harekrishna@gmail.com"]
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10
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s.homepage = "http://github.com/audy/lederhosen"
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11
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s.summary = '16S rRNA clustering for paired-end Illumina'
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s.description = 'Cluster 16S rRNA amplicon data sequenced by paired-end Illumina into OTUs. Also, quality control data first!'
|
13
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-
|
14
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s.rubyforge_project = "lederhosen"
|
15
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-
|
16
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s.files = `git ls-files`.split("\n")
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17
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-
s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n")
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18
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s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
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19
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s.require_paths = ["lib"]
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20
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-
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-
s.add_dependency('dna')
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22
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s.add_dependency('thor')
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23
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s.add_dependency('progressbar')
|
24
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-
end
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data/lib/version.rb
DELETED
File without changes
|
File without changes
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