module CagnutBwa::CheckTools
Public Instance Methods
check_bwa(path, ref_path)
click to toggle source
# File lib/cagnut_bwa/check_tools.rb, line 9 def check_bwa path, ref_path check_tool_ver 'BWA' do `#{path} 2>&1 | grep Version | cut -f2 -d ' '` if path end end
check_bwa_index(tool_path, ref_path)
click to toggle source
# File lib/cagnut_bwa/check_tools.rb, line 15 def check_bwa_index tool_path, ref_path tool = 'Bwa Index' file = "#{ref_path}.ann" command = "#{tool_path} index #{ref_path}" check_ref_related file, tool, command end
check_tool(tools_path, refs=nil)
click to toggle source
Calls superclass method
# File lib/cagnut_bwa/check_tools.rb, line 3 def check_tool tools_path, refs=nil super if defined?(super) ver = check_bwa tools_path['bwa'], refs['ref_fasta'] check_bwa_index tools_path['bwa'], refs['ref_fasta'] if !ver.blank? end