def test(self): config = parse_pipeline_config(self.cfg_file) self.assertEqual(config['SPADES_EXEC'], "$HOME/tools/SPAdes-3.0.0-Linux/bin/spades.py") self.assertEqual(config['SEQTK_EXEC'], "seqtk") self.assertEqual(config['QUAST_EXEC'], "$HOME/tools/quast-2.3/metaquast.py") self.assertEqual(config['R1_MARKER'], "_R1_") self.assertEqual(config['R2_MARKER'], "_R2_")
#!/usr/bin/env python import argparse from pipeline_lite.lib.utils import parse_pipeline_config from pipeline_lite.lib.assembly import assemble_directory def interface(): args = argparse.ArgumentParser() args.add_argument('-i', '--input-dir', help='Input directory', required=True) args.add_argument('-o', '--output-dir', help='Output directory', required=True) args.add_argument('-s', '--scripts-dir', help='Scripts directory', required=True) args.add_argument('-c', '--configuration-file', help='Pipeline configuration', default='pipeline.cfg') args = args.parse_args() return args if __name__=="__main__": args = interface() config = parse_pipeline_config(args.configuration_file) assemble_directory(args.input_dir, args.output_dir, args.scripts_dir, config)