# HG changeset patch # User dpryan79 # Date 1473933484 14400 # Node ID f5a15a12a4c9f9dab681ac85fd3f36f3683b8fd2 # Parent a801458261bb314f9e53de8fff90a68174c6f270 Uploaded diff -r a801458261bb -r f5a15a12a4c9 data_manager/bwameth_index_builder.py --- a/data_manager/bwameth_index_builder.py Thu Sep 15 04:59:28 2016 -0400 +++ b/data_manager/bwameth_index_builder.py Thu Sep 15 05:58:04 2016 -0400 @@ -11,14 +11,14 @@ DEFAULT_DATA_TABLE_NAME = "bwameth_indexes" -def build_hisat_index(data_manager_dict, params, args): +def build_bwameth_index(data_manager_dict, params, args): data_table_name = args.data_table_name target_directory = params[ 'output_data' ][0]['extra_files_path'] if not os.path.exists( target_directory ): os.mkdir( target_directory ) fasta_base_name = os.path.basename(args.fasta_filename) sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) - os.symlink(options.fasta_filename, sym_linked_fasta_filename) + os.symlink(args.fasta_filename, sym_linked_fasta_filename) args = ['bwameth.py', 'index', sym_linked_fasta_filename] proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait() @@ -55,7 +55,7 @@ raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey)) # build the index - build_hisat_index(data_manager_dict, args) + build_bwameth_index(data_manager_dict, params, args) # save info to json file open(filename, 'wb').write(dumps(data_manager_dict)) diff -r a801458261bb -r f5a15a12a4c9 data_manager/bwameth_index_builder.xml --- a/data_manager/bwameth_index_builder.xml Thu Sep 15 04:59:28 2016 -0400 +++ b/data_manager/bwameth_index_builder.xml Thu Sep 15 05:58:04 2016 -0400 @@ -1,6 +1,8 @@ builder + bwa + samtools bwameth + + + + + +