cagnut_snpeff 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 49567d185fa2c730ba7a3a37eec9ab4ef675f655
-  data.tar.gz: 1e36fdf1efa937f926624d850b96305c38b65151
+  metadata.gz: d0b4182b10716102b7e6393887c19618109dbe62
+  data.tar.gz: 2977d73203d236aa0e0596bf0767a027e444e379
 SHA512:
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+  metadata.gz: 6c9156c8f5fc9269d378841db34dc7e3eb22514be76f66ec1746c69d134a258c928614335bad1e6c282624fa0a4e250bac0fa71261a8aa01ec7508fdfbd6d754
+  data.tar.gz: abea750bd179b42e57496703610b52e47b442fab7a594975568c45a0fb9ec4ecb5318b92096fc49851719e4071d4e4e6c38fbd2f2d94fb546cc2b97a4ceb897d

data/lib/cagnut_snpeff.rb

@@ -12,5 +12,6 @@ module CagnutSnpeff
 end
 
 require 'cagnut_snpeff/configuration'
+require 'cagnut_snpeff/check_tools'
 require 'cagnut_snpeff/base'
 require 'cagnut_snpeff/util'

data/lib/cagnut_snpeff/check_tools.rb

@@ -1,30 +1,30 @@
 module CagnutSnpeff
   module CheckTools
-    def check_tool tools_path, ref=nil
+    def check_tool tools_path, refs=nil
       super if defined?(super)
-      check_snpeff tools['snpeff'], refs['snpeff']['db'], refs['snpeff']['config'] if @java
+      check_snpeff tools_path['snpeff'], refs['snpeff']['db'], refs['snpeff']['config'] if @java
     end
 
-      def check_snpeff path, db_version, config_path
-        check_tool_ver 'snpEff' do
-          `#{@java} -jar #{path} -version 2>&1` if path
-        end
+    def check_snpeff path, db_version, config_path
+      check_tool_ver 'snpEff' do
+        `#{@java} -jar #{path} -version 2>&1` if path
+      end
 
-        if db_version.nil?
-          @check_completed = false
-          puts "\tNot Set Snpeff DB in config.yml"
-        else
-          puts "\tSnpeff DB: #{db_version}"
-        end
+      if db_version.nil?
+        @check_completed = false
+        puts "\tNot Set Snpeff DB in config.yml"
+      else
+        puts "\tSnpeff DB: #{db_version}"
+      end
 
-        if config_path
-          path = File.exist?(config_path) ? config_path : 'Not Found' if config_path
-          puts "\tSnpeff config file: #{path}"
-        else
-          puts "\tSnpeff config Not Found"
-        end
+      if config_path
+        path = File.exist?(config_path) ? config_path : 'Not Found' if config_path
+        puts "\tSnpeff config file: #{path}"
+      else
+        puts "\tSnpeff config Not Found"
       end
+    end
   end
 end
 
-CagnutSnpeff.config::Checks::Tools.prepend CagnutSnpeff::CheckTools
+Cagnut::Configuration::Checks::Tools.prepend CagnutSnpeff::CheckTools

data/lib/cagnut_snpeff/version.rb

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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cagnut_snpeff
 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: cagnut_core