# Now we can run lucy several times, one for each library
        my $lib;my $in_s; my $in_q; my $vec; my $spli; my $out_s; my $out_q;
        for ($i=0;$i<$num_libraries;$i++){
                if ($success){  # if something went wrong we should stop
                        $lib=$libraries[$i];
                        $in_s=$in_seq."$separator".$libraries[$i];
                        $in_q=$in_qual."$separator".$libraries[$i];
                        my $num_lib=position1(@{$$assignments{libraries}},$lib);
                        $out_s=$out_seq."$separator".$libraries[$i];
                        $out_q=$out_qual."$separator".$libraries[$i];
                        #it could be libraries without vector and splice site information, in that case we just copy 
                        #the input file to the output file
                        if ($num_lib){
                                $vec=${$$assignments{vector_files}}[$num_lib-1];
                                $spli=${$$assignments{splice_files}}[$num_lib-1];
                                $success=run_lucy($config,$lib,$in_s,$in_q,$vec,$spli,$out_s,$out_q,$log,$bin_lucy);
                        }else{
                                print localtime().": WARNING there is no vector and splice information in the assignment file for the library $lib\n";
                                system ("ln -sf $in_s $out_s\n");
                                system ("ln -sf $in_q $out_q\n");
                                system ('echo "'.$lib.'" >> '.$not_lucy);
                        }
                }
        }


##</code><code>##

assignment
library: gammarus
vector file: /home/sbi6dap/est2uni/data/vector.fasta
vector splice site file: /home/sbi6dap/est2uni/data/splice.fasta