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comparison defuse.xml @ 12:33e2235bf003

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Add create_reference_dataset.xml
author Jim Johnson <jj@umn.edu>
date Sun, 09 Jun 2013 20:30:21 -0500
parents 08e9244aeab8
children 547d8db4673e
comparison
equal deleted inserted replaced
11:19c48803a377 12:33e2235bf003
224 # Directory where you want your dataset 224 # Directory where you want your dataset
225 gmap_index_directory = #slurp 225 gmap_index_directory = #slurp
226 #try 226 #try
227 $ref_dict['gmap_index_directory'] 227 $ref_dict['gmap_index_directory']
228 #except 228 #except
229 \$(dataset_directory)/gmap 229 #raw
230 $(dataset_directory)/gmap
231 #end raw
230 #end try 232 #end try
231 233
232 #raw 234 #raw
233 # Dataset files 235 # Dataset files
234 dataset_prefix = $(dataset_directory)/defuse 236 dataset_prefix = $(dataset_directory)/defuse
595 ln -s $defuse_out.extra_files_path output_dir 597 ln -s $defuse_out.extra_files_path output_dir
596 #else 598 #else
597 mkdir -p output_dir 599 mkdir -p output_dir
598 #end if 600 #end if
599 ## run defuse.pl 601 ## run defuse.pl
600 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -d data_dir -o output_dir -p 8 602 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p 8
601 ## copy primary results to output datasets 603 ## copy primary results to output datasets
602 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi 604 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
603 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi 605 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
604 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi 606 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
605 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi 607 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi