def run
      if @options[:list_assemblers]
        puts @assemblerman.list_assemblers
        return
      elsif @options[:install_assemblers]
        @assemblerman.install_assemblers(@options[:install_assemblers])
        return
      end

      if (@options[:left].nil? || @options[:right].nil?)
        logger.error "Reads must be provided with --left and --right"
        logger.error "Try --help for command-line help"
        exit(1)
      end

      unless (@options[:timelimit].nil?)
        logger.info "Time limit set to #{@options[:timelimit]}"
      end

      subsample_input

      res = @assemblerman.run_all_assemblers @options
      write_metadata res
      merge_assemblies res

    end
def run
      if @options[:list_assemblers]
        puts @assemblerman.list_assemblers
        return
      elsif @options[:install_assemblers]
        @assemblerman.install_assemblers(@options[:install_assemblers])
        return
      end

      if (@options[:left].nil? || @options[:right].nil?)
        logger.error "Reads must be provided with --left and --right"
        logger.error "Try --help for command-line help"
        exit(1)
      end

      unless (@options[:timelimit].nil?)
        logger.info "Time limit set to #{@options[:timelimit]}"
      end

      subsample_input

      res = @assemblerman.run_all_assemblers @options
      write_metadata res
      merge_assemblies res

    end
Runs the program