lederhosen 0.2.8 → 0.2.9

data/lederhosen.gemspec

@@ -0,0 +1,93 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "lederhosen"
+  s.version = "0.2.9"
+
+  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.description = "Various tools for OTU clustering"
+  s.email = "harekrishna@gmail.com"
+  s.executables = ["lederhosen"]
+  s.files = [
+    ".rspec",
+    ".rvmrc",
+    "Gemfile",
+    "Rakefile",
+    "bin/lederhosen",
+    "examples/hierarchical_clustering.sh",
+    "examples/pipeline.sh",
+    "lederhosen.gemspec",
+    "lib/lederhosen.rb",
+    "lib/lederhosen/buffer.rb",
+    "lib/lederhosen/cli.rb",
+    "lib/lederhosen/helpers.rb",
+    "lib/lederhosen/tasks/add_names.rb",
+    "lib/lederhosen/tasks/cluster.rb",
+    "lib/lederhosen/tasks/join.rb",
+    "lib/lederhosen/tasks/k_filter.rb",
+    "lib/lederhosen/tasks/name.rb",
+    "lib/lederhosen/tasks/otu_filter.rb",
+    "lib/lederhosen/tasks/otu_table.rb",
+    "lib/lederhosen/tasks/rep_reads.rb",
+    "lib/lederhosen/tasks/sort.rb",
+    "lib/lederhosen/tasks/split.rb",
+    "lib/lederhosen/tasks/squish.rb",
+    "lib/lederhosen/tasks/trim.rb",
+    "lib/lederhosen/tasks/uc_filter.rb",
+    "lib/lederhosen/tasks/uc_stats.rb",
+    "lib/lederhosen/tasks/uniquify.rb",
+    "lib/lederhosen/version.rb",
+    "readme.md",
+    "spec/cli_spec.rb",
+    "spec/data/ILT_L_9_B_001_1.txt.gz",
+    "spec/data/ILT_L_9_B_001_3.txt.gz",
+    "spec/data/ILT_L_9_B_002_1.txt.gz",
+    "spec/data/ILT_L_9_B_002_3.txt.gz",
+    "spec/data/blat.txt",
+    "spec/data/otus.csv",
+    "spec/helpers_spec.rb",
+    "spec/misc_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://github.com/audy/lederhosen"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.24"
+  s.summary = "OTU Clustering"
+
+  if s.respond_to? :specification_version then
+    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<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"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+    else
+      s.add_dependency(%q<dna>, [">= 0"])
+      s.add_dependency(%q<progressbar>, [">= 0"])
+      s.add_dependency(%q<thor>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<dna>, [">= 0"])
+    s.add_dependency(%q<progressbar>, [">= 0"])
+    s.add_dependency(%q<thor>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+  end
+end
+

data/lib/lederhosen/cli.rb

@@ -5,7 +5,7 @@ module Lederhosen
     no_tasks do
       # just print string to STDERR
       def ohai(s)
-        @shell.say(s)
+        @shell.say_status('okay', s, 'green')
       end
     end
 

data/lib/lederhosen/tasks/add_names.rb

@@ -79,7 +79,7 @@ module Lederhosen
       end
 
       # print status message
-      ohai "Got #{clusterid_to_name.keys.reject { |x| x =~ /cluster/ }.size} names (#{clusterid_to_name.keys.size} total)"
+      ohai "Got #{clusterid_to_name.values.reject { |x| x =~ /cluster/ }.size} names (#{clusterid_to_name.keys.size} total)"
     end
 
   end

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 2
-    PATCH = 8
+    PATCH = 9
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 7
+  hash: 5
   prerelease: 
   segments: 
   - 0
   - 2
-  - 8
-  version: 0.2.8
+  - 9
+  version: 0.2.9
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-08-07 00:00:00 Z
+date: 2012-08-08 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :runtime
@@ -130,6 +130,9 @@ files:
 - Gemfile
 - Rakefile
 - bin/lederhosen
+- examples/hierarchical_clustering.sh
+- examples/pipeline.sh
+- lederhosen.gemspec
 - lib/lederhosen.rb
 - lib/lederhosen/buffer.rb
 - lib/lederhosen/cli.rb
@@ -150,8 +153,6 @@ files:
 - lib/lederhosen/tasks/uc_stats.rb
 - lib/lederhosen/tasks/uniquify.rb
 - lib/lederhosen/version.rb
-- pipelines/hierarchical_clustering.sh
-- pipelines/pipeline.sh
 - readme.md
 - spec/cli_spec.rb
 - spec/data/ILT_L_9_B_001_1.txt.gz