Mercurial > repos > jjohnson > defuse
comparison defuse.xml @ 13:3a4876d01c7e draft
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 12 Dec 2017 10:01:42 -0500 |
| parents | 4fe2e80d4ae1 |
| children | bdd93719cede |
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| 12:4fe2e80d4ae1 | 13:3a4876d01c7e |
|---|---|
| 624 ln -s $defuse_out.dataset.extra_files_path output_dir | 624 ln -s $defuse_out.dataset.extra_files_path output_dir |
| 625 #else | 625 #else |
| 626 mkdir -p output_dir | 626 mkdir -p output_dir |
| 627 #end if | 627 #end if |
| 628 ## run defuse.pl | 628 ## run defuse.pl |
| 629 perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS | 629 perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS; |
| 630 exit_code_for_galaxy=\$?; | |
| 630 ## copy primary results to output datasets | 631 ## copy primary results to output datasets |
| 631 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi | 632 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi |
| 632 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi | 633 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi |
| 633 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi | 634 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi |
| 634 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi | 635 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi |
| 664 then | 665 then |
| 665 mkdir -p $fusion_reads.dataset.extra_files_path | 666 mkdir -p $fusion_reads.dataset.extra_files_path |
| 666 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path | 667 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path |
| 667 fi | 668 fi |
| 668 #end if | 669 #end if |
| 670 (exit \$exit_code_for_galaxy) | |
| 669 </configfile> | 671 </configfile> |
| 670 </configfiles> | 672 </configfiles> |
| 671 | 673 |
| 672 <tests> | 674 <tests> |
| 673 </tests> | 675 </tests> |