module CagnutPicard::CheckTools

Public Instance Methods

check_Picard(path) click to toggle source
# File lib/cagnut_picard/check_tools.rb, line 9
def check_Picard path
  check_tool_ver 'Picard' do
    `#{@java} -jar #{path} AddOrReplaceReadGroups --version 2>&1` if path
  end
end
check_picard_dict(ref_path) click to toggle source
# File lib/cagnut_picard/check_tools.rb, line 15
def check_picard_dict ref_path
  tool = 'Sequence Dictionary'
  file = ref_path.gsub '.fasta', '.dict'
  command =
    "#{@java} -jar #{@config['tools']['picard']} CreateSequenceDictionary REFERENCE=#{ref_path} OUTPUT=#{file}"
  check_ref_related file, tool, command
end
check_tool(tools_path, refs=nil) click to toggle source
Calls superclass method
# File lib/cagnut_picard/check_tools.rb, line 3
def check_tool tools_path, refs=nil
  super if defined?(super)
  ver = check_Picard tools_path['picard'] if @java
  check_picard_dict refs['ref_fasta'] if !ver.blank?
end