bio-rocker 1.1.10 → 1.1.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e05b58cc0291bee319fcc3b154922e9b258f0c8b
-  data.tar.gz: d3780e512d02ef04c60696a01f8c736b61703707
+  metadata.gz: 85c453e6a8e2ced8f03b930ea696682b11a90c5c
+  data.tar.gz: 64e2894fdb38450bd3849168825d2a75cdac960f
 SHA512:
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-  data.tar.gz: c6025ff319794cd9fbc7b52f2a019bb5021fe0474b9536270d9eaf72385738db11d965676201d6440c1b6dceacfb851bb9f31e909c33d04e93f2308b2fc6cf01
+  metadata.gz: db06cca064320b559290ac7ecb5aad40e89bc4bab30cd69510e4f537b834d863ab4b7fbe64885790d181246a033fabfd6184667b2bb10841a00b5908c8addd91
+  data.tar.gz: 574a1ab17ec2fc44a7993eba843c193db2c8acb7ed56e52429436d2b9a03162f6c0f540d715eff73de2e145a85e7c76c6a1bd424d1d1e9a759d465eacea23a41

data/bin/ROCker

@@ -1,10 +1,9 @@
 #!/usr/bin/env ruby
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @author Luis (Coto) Orellana
+
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author  Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Nov-25-2015
-#
+# @update  Mar-28-2016
 
 lib = File.expand_path("../lib", File.dirname(__FILE__))
 $:.push lib if Dir.exist? lib
@@ -26,8 +25,13 @@ $t = {
    		"thresholds, and the hits.",
    "info"    =>	"Display additional information about ROCker."
 }
-task = (ARGV.empty? ? "" : ARGV.shift).downcase
-ARGV << "-h" if ARGV.empty? and task != "info"
+
+if %w[-V --version].include? ARGV.first
+   task = "info"
+else
+   task = (ARGV.empty? ? "" : ARGV.shift).downcase
+   ARGV << "-h" if ARGV.empty? and task != "info"
+end
 
 o = {}
 opts = OptionParser.new do |opt|
@@ -324,10 +328,14 @@ opts = OptionParser.new do |opt|
    opt.on("-q", "--quiet", "Run quietly."){ |v| o[:q]=true }
    opt.on("-d", "--debug",
       "Display debugging information."){ |v| o[:debug]=true }
-   opt.on("-h", "--help", "Display this screen") do
+   opt.on("-h", "--help", "Display this screen.") do
       puts opt
       exit
    end
+   opt.on("-V", "--version","Display version.") do
+      puts "ROCker v" + ROCker.VERSION
+      exit
+   end
    opt.separator ""
    unless $t.include? task
       puts opt
@@ -336,6 +344,8 @@ opts = OptionParser.new do |opt|
 end
 opts.parse!
 
+p ARGV
+
 
 #================================[ Main ]
 rocker = ROCker.new(o)
@@ -363,7 +373,7 @@ begin
       puts "For additional information and documentation, visit:"
       puts "http://enve-omics.ce.gatech.edu/rocker/"
       puts ""
-      puts "For our list of curated models, visits:"
+      puts "For our list of curated models, visit:"
       puts "http://enve-omics.ce.gatech.edu/rocker/models"
    end
 rescue => err

data/lib/rocker.rb

@@ -10,7 +10,7 @@ require "rocker/rocdata"
 
 class ROCker
    #================================[ Class ]
-   @@VERSION = "1.1.10"
+   @@VERSION = "1.1.11"
    @@CITATION = [
       "Orellana, Rodriguez-R, & Konstantinidis. Under review.",
       "Detecting and quantifying functional genes in short-read",

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.1.10
+  version: 1.1.11
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -15,28 +15,28 @@ dependencies:
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.7'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.8'
 description: Detecting and quantifying functional genes in short-read metagenomic
@@ -47,21 +47,21 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- bin/ROCker
 - lib/rocker.rb
+- lib/rocker/sequence.rb
 - lib/rocker/alignment.rb
 - lib/rocker/blasthit.rb
+- lib/rocker/rocwindow.rb
+- lib/rocker/rocdata.rb
+- lib/rocker/rinterface.rb
 - lib/rocker/genome-set.rb
 - lib/rocker/protein-set.rb
-- lib/rocker/rinterface.rb
-- lib/rocker/rocdata.rb
-- lib/rocker/rocwindow.rb
-- lib/rocker/sequence.rb
 - lib/rocker/step/build.rb
 - lib/rocker/step/compile.rb
+- lib/rocker/step/search.rb
 - lib/rocker/step/filter.rb
 - lib/rocker/step/plot.rb
-- lib/rocker/step/search.rb
+- bin/ROCker
 homepage: http://enve-omics.ce.gatech.edu/rocker
 licenses:
 - artistic 2.0
@@ -72,17 +72,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '2.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5.1
+rubygems_version: 2.0.14
 signing_key: 
 specification_version: 4
 summary: ROCker