lederhosen 0.3.0 → 0.3.1

data/Gemfile

@@ -1,6 +1,6 @@
 source :rubygems
 
-gem 'dna'
+gem 'dna', '0.0.12'
 gem 'progressbar'
 gem 'thor'
 

data/LICENSE.txt

@@ -0,0 +1,7 @@
+Copyright (C) 2012 Austin G. Davis-Richardson
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Rakefile

@@ -17,7 +17,7 @@ require 'rake'
 require 'jeweler'
 Jeweler::Tasks.new do |gem|
   gem.name = "lederhosen"
-  gem.homepage = "http://github.com/audy/lederhosen"
+  gem.homepage = "http://audy.github.com/lederhosen"
   gem.license = "MIT"
   gem.summary = "OTU Clustering"
   gem.description = "Various tools for OTU clustering"

data/lederhosen.gemspec

@@ -5,18 +5,22 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "0.3.0"
+  s.version = "0.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-08-08"
+  s.date = "2012-08-12"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt"
+  ]
   s.files = [
     ".rspec",
     ".rvmrc",
     "Gemfile",
+    "LICENSE.txt",
     "Rakefile",
     "bin/lederhosen",
     "examples/hierarchical_clustering.sh",
@@ -55,7 +59,7 @@ Gem::Specification.new do |s|
     "spec/misc_spec.rb",
     "spec/spec_helper.rb"
   ]
-  s.homepage = "http://github.com/audy/lederhosen"
+  s.homepage = "http://audy.github.com/lederhosen"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
   s.rubygems_version = "1.8.24"
@@ -65,14 +69,14 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<dna>, [">= 0"])
+      s.add_runtime_dependency(%q<dna>, ["= 0.0.12"])
       s.add_runtime_dependency(%q<progressbar>, [">= 0"])
       s.add_runtime_dependency(%q<thor>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, [">= 0"])
       s.add_development_dependency(%q<jeweler>, [">= 0"])
     else
-      s.add_dependency(%q<dna>, [">= 0"])
+      s.add_dependency(%q<dna>, ["= 0.0.12"])
       s.add_dependency(%q<progressbar>, [">= 0"])
       s.add_dependency(%q<thor>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
@@ -80,7 +84,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, [">= 0"])
     end
   else
-    s.add_dependency(%q<dna>, [">= 0"])
+    s.add_dependency(%q<dna>, ["= 0.0.12"])
     s.add_dependency(%q<progressbar>, [">= 0"])
     s.add_dependency(%q<thor>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 3
-    PATCH = 0
+    PATCH = 1
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -2,6 +2,10 @@
 
 Cluster raw Illumina 16S rRNA amplicon data to generate OTUs.
 
+## Who can use Lederhosen?
+
+Lederhosen is free and open source under the [MIT open source license](http://opensource.org/licenses/mit-license.php/)
+
 ## How do I get Lederhosen?
 
 0. Obtain & Install [UCLUST](http://www.drive5.com/) (64-bit)

data/spec/cli_spec.rb

@@ -37,7 +37,7 @@ describe Lederhosen::CLI do
   end
 
   it 'should build OTU abundance matrices' do
-    `./bin/lederhosen otu_table --clusters=#{$test_dir}/clusters.uc --output=#{$test_dir}/test_tables --joined=#{$test_dir}/joined.fasta`
+    `./bin/lederhosen otu_table --clusters=#{$test_dir}/clusters.uc --output=#{$test_dir}/test_tables`
     $?.success?.should be_true
   end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 17
   prerelease: 
   segments: 
   - 0
   - 3
-  - 0
-  version: 0.3.0
+  - 1
+  version: 0.3.1
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,19 +15,21 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-08-08 00:00:00 Z
+date: 2012-08-12 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :runtime
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - "="
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 7
         segments: 
         - 0
-        version: "0"
+        - 0
+        - 12
+        version: 0.0.12
   version_requirements: *id001
   name: dna
   prerelease: false
@@ -108,12 +110,13 @@ executables:
 - lederhosen
 extensions: []
 
-extra_rdoc_files: []
-
+extra_rdoc_files: 
+- LICENSE.txt
 files: 
 - .rspec
 - .rvmrc
 - Gemfile
+- LICENSE.txt
 - Rakefile
 - bin/lederhosen
 - examples/hierarchical_clustering.sh
@@ -151,7 +154,7 @@ files:
 - spec/helpers_spec.rb
 - spec/misc_spec.rb
 - spec/spec_helper.rb
-homepage: http://github.com/audy/lederhosen
+homepage: http://audy.github.com/lederhosen
 licenses: 
 - MIT
 post_install_message: