import sys
import re
from gaworkflow.pipeline.configure_run import *
-from gaworkflow.pipeline import retrieve_config
+from gaworkflow.pipeline import retrieve_config as _rc
from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
s_fc = re.compile('FC[0-9]+')
#Turn on built-in command-line parsing.
-retrieve_config.DISABLE_CMDLINE = False
+_rc.DISABLE_CMDLINE = False
GENOME_DIR = '/data-store01/compbio/genomes/'
def main(args=None):
ci = ConfigInfo()
+ ci.analysis_dir = os.getcwd()
+ ci.base_analysis_dir, junk = os.path.split(ci.analysis_dir)
#FIXME: make a better command line tool
skip_retrieve_config = False