lederhosen 3.2.0 → 3.2.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: d4f049c98435fbc48c6b5d7f399346d05c5f0847
+  data.tar.gz: 048cc246fd1eee492f9d74179622197451f8496a
+SHA512:
+  metadata.gz: 7d3faf78771049bafbfd3227391dd1729001cf18e6f9eab358ef058c9f52cee7cf78722c5250f54bc22d804deaf4446b4e56402af737f9a1603a8e4c624cba4f
+  data.tar.gz: 72740fa34f9eb725616c548cf68ba42ebcb0284e6c023ed4c5bb70151841ae3ecc311c09fdaba87d70ac849d8ddcfc3d4da8a548d6aeb4f4a990d90cdba75680

data/.travis.yml

@@ -1,3 +1,4 @@
 rvm:
-  - '1.9.7'
+  - 1.9.3
+  - 2.0.0
 script: bundle exec rspec

data/Gemfile

@@ -4,12 +4,12 @@ gem 'dna', '0.3.0'
 gem 'progressbar', '0.12.0'
 gem 'thor', '0.16.0'
 
-group :test do
-  gem 'rspec', '2.12.0'
-  gem 'pry'
-end
-
 group :development do
-  gem 'rdoc', '~> 3.12'
   gem 'jeweler', '1.8.4'
+  gem 'rdoc', '~> 3.12'
+end
+
+group :test do
+  gem 'pry'
+  gem 'rspec', '2.12.0'
 end

data/lederhosen.gemspec

@@ -2,14 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: lederhosen 3.2.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "3.2.0"
+  s.version = "3.2.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2013-08-02"
+  s.date = "2014-04-16"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]
@@ -57,32 +59,31 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://audy.github.com/lederhosen"
   s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.25"
+  s.rubygems_version = "2.2.2"
   s.summary = "OTU Clustering"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<dna>, ["= 0.3.0"])
       s.add_runtime_dependency(%q<progressbar>, ["= 0.12.0"])
       s.add_runtime_dependency(%q<thor>, ["= 0.16.0"])
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<jeweler>, ["= 1.8.4"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
     else
       s.add_dependency(%q<dna>, ["= 0.3.0"])
       s.add_dependency(%q<progressbar>, ["= 0.12.0"])
       s.add_dependency(%q<thor>, ["= 0.16.0"])
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<jeweler>, ["= 1.8.4"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
     end
   else
     s.add_dependency(%q<dna>, ["= 0.3.0"])
     s.add_dependency(%q<progressbar>, ["= 0.12.0"])
     s.add_dependency(%q<thor>, ["= 0.16.0"])
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<jeweler>, ["= 1.8.4"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
   end
 end
 

data/lib/lederhosen.rb

@@ -3,4 +3,8 @@ require 'dna'
 require 'progressbar'
 require 'thor'
 
-Dir.glob(File.join(File.dirname(__FILE__), 'lederhosen', '*.rb')).each { |f| require f }
+# files have to be required in order.
+# changes depending on system.
+%w{cli no_tasks uc_parser version}.each do |f|
+  require File.join(File.dirname(__FILE__), 'lederhosen', "#{f}.rb")
+end

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 3
     MINOR = 2
     CODENAME = 'Tandem-Fahrrad' # changes for minor versions
-    PATCH = 0
+    PATCH = 1
 
     string = [MAJOR, MINOR, PATCH].join('.')
 

data/readme.md

@@ -29,7 +29,7 @@ the USEARCH license, Lederhosen is free for commercial use.
 
 Tested using Ruby 1.9.3 and 2.0.0 (1.8.7 not supported)
 
-0. Obtain & Install [USEARCH](http://www.drive5.com/).
+0. Obtain & Install [USEARCH](http://www.drive5.com/) version 7.
 1. Get a database:
   - [TaxCollector](http://github.com/audy/taxcollector)
   - [GreenGenes 13.5 Rep. Set](http://greengenes.secondgenome.com/downloads) 16S
@@ -90,11 +90,11 @@ do
     echo lederhosen cluster \
                     --input=$reads_file \
                     --identity=0.95 \
-                    --output=$(basename $reads_file_ .fasta).95.uc \
+                    --output=$(basename $reads_file .fasta).95.uc \
                     --database=taxcollector.udb \
                     --threads 1 \
                     --dry-run
-end > jobs.sh
+done > jobs.sh
 
 # send jobs to queue system
 cat jobs.sh | parallel -j 24 # run 24 parallel jobs

data/spec/no_tasks_spec.rb

@@ -1,6 +1,6 @@
 require 'spec_helper'
 
-describe 'no_tasks' do
+describe 'Lederhosen::CLI.no_tasks' do
 
   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']}
   let(:greengenes135_taxonomies) { ['k__domain; p__phylum; c__class; o__order; f__family; g__genus; s__species']}

data/spec/spec_helper.rb

@@ -2,6 +2,8 @@ $:.unshift File.join(File.dirname(__FILE__), '..')
 
 require 'lederhosen'
 
+require 'bundler'
+
 Bundler.require :test, :development
 
 $test_dir = ENV['TEST_DIR'] || "/tmp/lederhosen_test_#{(0...8).map{65.+(rand(25)).chr}.join}/"

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 3.2.0
-  prerelease: 
+  version: 3.2.1
 platform: ruby
 authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-02 00:00:00.000000000 Z
+date: 2014-04-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dna
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -30,7 +27,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: progressbar
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -38,7 +34,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -46,7 +41,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: thor
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -54,43 +48,38 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.16.0
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - '='
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: 1.8.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - '='
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: 1.8.4
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '3.12'
 description: Various tools for OTU clustering
 email: harekrishna@gmail.com
 executables:
@@ -99,8 +88,8 @@ extensions: []
 extra_rdoc_files:
 - LICENSE.txt
 files:
-- .rspec
-- .travis.yml
+- ".rspec"
+- ".travis.yml"
 - Gemfile
 - LICENSE.txt
 - Rakefile
@@ -139,29 +128,25 @@ files:
 homepage: http://audy.github.com/lederhosen
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -502231150747974462
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: OTU Clustering
 test_files: []