lib/bio/pipengine/job.rb
# this method call other methods to perform the right substitutions into the command lines
this method call other methods to perform the right substitutions into the command lines
this method call other methods to perform the right substitutions into the command lines
def generate_cmd_line(cmd,sample,step)
				if step.is_multi? 
					set_multi_cmd(step,self.multi_samples)
					cmd = sub_multi(cmd,step)
				else
					cmd = sub_placeholders(cmd,sample,step) 
				end
				cmd.scan(/<\S+>/).each do |unsubstituted_tag|
					@@logger_error.error("Found an unsubstituted tag #{unsubstituted_tag} . Terminating the execution".red)
					exit
				end
				return cmd
			end
def generate_cmd_line ( cmd , sample , step ) if step . is_multi? set_multi_cmd ( step , self . multi_samples ) cmd = sub_multi ( cmd , step ) else cmd = sub_placeholders ( cmd , sample , step ) end cmd . scan ( / < \S +> / ) . each do | unsubstituted_tag | @@logger_error . error ( "Found an unsubstituted tag #{unsubstituted_tag} . Terminating the execution" . red ) exit end return cmd end
this method call other methods to perform the right substitutions into the command lines
this method call other methods to perform the right substitutions into the command lines
# if is a multi samples step call a different method # normal step, perform usual substitutions # Check that all placeholders have been substituted, if not terminate with an error
cmd
<not_specific>
sample
<not_specific>
step
<not_specific>