cagnut_core 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e8f656425110b7d2bc1fbee6c89d45b97301e0b9
-  data.tar.gz: 056d7b62798bdc1254827276631111f1e2edbe49
+  metadata.gz: a3043c0169386288bb33ba28308bc79a662bfb06
+  data.tar.gz: d53e358ea09299895646b483dc43507545ac94a9
 SHA512:
-  metadata.gz: c7fe94d621066a84390cbb05bb9f300333fea02b44693190c446958286cd045d50529f821e648225132402843aa8c4b42aef4a61d607aad86a6f38eb1ba0611e
-  data.tar.gz: 3a271af722e943e1a3af6e35efe6bc2d1f057ad968e27397a78496d4666efaff0c5de5a85ba18b09df42638980c0e5d0c80dd4389e8e775c97d0d8b37caf6b8c
+  metadata.gz: 703c7e9017043a9aebd258a7bc6269135dd9d544de6b6dcbfd32d07b55b670311fe64c149cc26bcabe82ba18452342a251e4391862ac615e351e6dc62f86ed15
+  data.tar.gz: a5a0550a1f044d42a0b8bcf3b2d8395fd75b109b348d6386415dd5e74f355a70f7e16c20b2169394ed29a787f3b79ee2da20e63f450e00241989e352a3f87b53

data/lib/cagnut/cli/pipeline.rb

@@ -28,6 +28,8 @@ module Cagnut
         end
       end
 
+      private
+
       def get_config_name pipeline_names
         abort 'Did not assign pipeline to run' if pipeline_names.blank?
         selected = self.class.pipelines.find do |p|

data/lib/cagnut/configuration/checks/tools.rb

@@ -20,20 +20,24 @@ module Cagnut
           tools = @config['tools']
           refs = @config['refs']
           puts 'Start Checking...'
-          check_queueing_system @config['queueing_system']
+          check_execute_system
           check_ref_fasta refs['ref_fasta']
           check_java tools['java']
           check_r tools['R']
           check_tool tools, refs
         end
 
+        def check_execute_system
+          puts "Using Local System"
+        end
+
         def check_tool tools_path, refs=nil
         end
 
         def check_tool_ver tool
           ver = yield if block_given?
-          @check_completed = false if ver.nil?
-          ver = ver.nil? ? 'Not Found' : ver.chomp!
+          @check_completed = false if ver.blank?
+          ver = ver.blank? ? 'Not Found' : ver.chomp!
           puts "Using #{tool} (#{ver})"
         end
 
@@ -59,11 +63,6 @@ module Cagnut
           end
         end
 
-        def check_queueing_system queueing_system
-          system = queueing_system.nil? ? 'Local' : queueing_system['system']
-          puts "Using Queueing System: #{system}"
-        end
-
         def check_ref_fasta ref_path
           puts 'Checking Reference Files...'
           return if File.exist?(ref_path)

data/lib/cagnut/configuration.rb

@@ -28,7 +28,7 @@ module Cagnut
       def load_config config_name, options
         @config ||= check_and_load_yml fetch_system_config_path(options[:config])
         @params ||= check_and_load_yml fetch_tools_config_path(config_name, options[:params])
-        config_check config_name, options[:not_check]
+        config_check config_name, options[:no_check]
       end
 
       private

data/lib/cagnut/version.rb

@@ -1,3 +1,3 @@
 module CagnutCore
-  VERSION = "0.3.0"
+  VERSION = "0.3.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cagnut_core
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
 platform: ruby
 authors:
 - Shi-Gang Wang
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-11-01 00:00:00.000000000 Z
+date: 2016-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport