Mercurial > repos > devteam > data_manager_bowtie2_index_builder
diff data_manager/bowtie2_index_builder.py @ 4:d1d5feb31804 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
| author | iuc |
|---|---|
| date | Thu, 09 May 2019 16:15:47 -0400 |
| parents | 83da94c0e4a6 |
| children | 1c0f8e9d87c6 |
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--- a/data_manager/bowtie2_index_builder.py Tue Apr 04 18:06:10 2017 -0400 +++ b/data_manager/bowtie2_index_builder.py Thu May 09 16:15:47 2019 -0400 @@ -31,6 +31,9 @@ sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) os.symlink( fasta_filename, sym_linked_fasta_filename ) args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ] + threads = os.environ.get('GALAXY_SLOTS') + if threads: + args.extend(['--threads', threads]) proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait() if return_code: @@ -74,7 +77,8 @@ build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES ) # save info to json file - open( filename, 'wb' ).write( dumps( data_manager_dict ) ) + with open(filename, 'w') as json_out: + json_out.write( dumps( data_manager_dict, sort_keys=True ) ) if __name__ == "__main__":