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)