6 logging.basicConfig(level=logging.DEBUG,
7 format='%(asctime)s %(levelname)-8s %(message)s',
8 datefmt='%a, %d %b %Y %H:%M:%S',
9 filename='config_pipeline.log',
13 s_start = re.compile('Starting Genome Analyzer Pipeline')
14 s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
15 s_generating = re.compile('Generating journals, Makefiles and parameter files')
18 s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
21 s_skip = re.compile('s_[0-8]_[0-9]+')
26 if s_skip.search(line):
28 elif s_invalid_cmdline.search(line):
29 logging.error("Invalid commandline options!")
30 elif s_start.search(line):
31 logging.info('START: Configuring pipeline')
32 elif s_gerald.search(line):
33 logging.info('Running make now')
34 elif s_generating.search(line):
35 logging.info('Make files generted')
37 logging.warning('How to handle: %s' % (line))
42 #pipe = subprocess.Popen(['goat_pipeline.py',
43 # '--GERALD=config32bk.txt',
46 # stdout=subprocess.PIPE,
47 # stderr=subprocess.PIPE)
49 #Not a test; actual run attempt.
50 pipe = subprocess.Popen(['goat_pipeline.py',
51 '--GERALD=config32bk.txt',
54 stdout=subprocess.PIPE,
55 stderr=subprocess.PIPE)
57 line = pipe.stdout.readline()
61 line = pipe.stdout.readline()
66 if __name__ == '__main__':