--- /dev/null
+#!/usr/bin/python
+import subprocess
+import re
+import logging
+
+logging.basicConfig(level=logging.DEBUG,
+ format='%(asctime)s %(levelname)-8s %(message)s',
+ datefmt='%a, %d %b %Y %H:%M:%S',
+ filename='config_pipeline.log',
+ filemode='w')
+
+#Info
+s_start = re.compile('Starting Genome Analyzer Pipeline')
+s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
+s_generating = re.compile('Generating journals, Makefiles and parameter files')
+
+#Errors
+s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
+
+#Ignore
+s_skip = re.compile('s_[0-8]_[0-9]+')
+
+def handler(line):
+
+ # Irrelevant line
+ if s_skip.search(line):
+ pass
+ elif s_invalid_cmdline.search(line):
+ logging.error("Invalid commandline options!")
+ elif s_start.search(line):
+ logging.info('START: Configuring pipeline')
+ elif s_gerald.search(line):
+ logging.info('Running make now')
+ elif s_generating.search(line):
+ logging.info('Make files generted')
+ else:
+ logging.warning('How to handle: %s' % (line))
+
+
+def configure():
+ #ERROR Test:
+ #pipe = subprocess.Popen(['goat_pipeline.py',
+ # '--GERALD=config32bk.txt',
+ # '--make .',],
+ # #'.'],
+ # stdout=subprocess.PIPE,
+ # stderr=subprocess.PIPE)
+
+ #Not a test; actual run attempt.
+ pipe = subprocess.Popen(['goat_pipeline.py',
+ '--GERALD=config32bk.txt',
+ '--make',
+ '.'],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+
+ line = pipe.stdout.readline()
+
+ while line != '':
+ handler(line)
+ line = pipe.stdout.readline()
+
+ #print pipe.poll()
+
+
+if __name__ == '__main__':
+ configure()