class Cagnut::Configuration::Checks::Tools
Attributes
check_completed[RW]
config[RW]
java[RW]
Public Class Methods
new(config)
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# File lib/cagnut/configuration/checks/tools.rb, line 7 def initialize config @config = config end
Public Instance Methods
check()
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# File lib/cagnut/configuration/checks/tools.rb, line 11 def check @check_completed = true check_each_tool result = @check_completed ? 'Completed!' : 'Failed!' puts "Check Tools: #{result}" exit unless @check_completed end
check_each_tool()
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# File lib/cagnut/configuration/checks/tools.rb, line 19 def check_each_tool tools = @config['tools'] refs = @config['refs'] puts 'Start Checking...' check_execute_system check_ref_fasta refs['ref_fasta'] check_java tools['java'] check_r tools['R'] check_tool tools, refs end
check_execute_system()
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# File lib/cagnut/configuration/checks/tools.rb, line 30 def check_execute_system puts "Using Local System" end
check_java(path)
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# File lib/cagnut/configuration/checks/tools.rb, line 44 def check_java path failed = check_tool_ver 'Java' do `#{path} -version 2>&1| grep version | cut -f3 -d ' '` if path end @java = path unless failed end
check_r(path)
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# File lib/cagnut/configuration/checks/tools.rb, line 51 def check_r path check_tool_ver 'R' do `#{path} --version 2>&1 |grep ' version '| cut -f3 -d ' '` if path end check_r_libs path if path end
check_r_libs(r_path)
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# File lib/cagnut/configuration/checks/tools.rb, line 58 def check_r_libs r_path %w(gplots ggplot2 reshape gsalib).each do |lib| check_tool_ver "R library: #{lib}" do `#{r_path}script -e 'packageVersion("#{lib}")' | cut -f2 -d ' '` end end end
check_ref_fasta(ref_path)
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# File lib/cagnut/configuration/checks/tools.rb, line 66 def check_ref_fasta ref_path puts 'Checking Reference Files...' return if File.exist?(ref_path) puts "\tReference not founded in #{ref_path}" @check_completed = false end
check_tool(tools_path, refs=nil)
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# File lib/cagnut/configuration/checks/tools.rb, line 34 def check_tool tools_path, refs=nil end
check_tool_ver(tool) { || ... }
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# File lib/cagnut/configuration/checks/tools.rb, line 37 def check_tool_ver tool ver = yield if block_given? @check_completed = false if ver.blank? ver = ver.blank? ? 'Not Found' : ver.chomp! puts "Using #{tool} (#{ver})" end