Improve code to extract runfolder name from the path to the runfolder.

[htsworkflow.git] / scripts / configure_pipeline

diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline
index c70f319beeebb54baef9446e47758b1d57b41fe7..6c94b914db834f1dcb5eb2d034591ed4ed19cb74 100644 (file)
--- a/scripts/configure_pipeline
+++ b/scripts/configure_pipeline
@@ -3,13 +3,19 @@ import os
 import sys
 import re
 from gaworkflow.pipeline.configure_run import *
-from gaworkflow.pipeline import retrieve_config
-from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
+from gaworkflow.pipeline import retrieve_config as _rc
+from gaworkflow.pipeline.run_status import startCmdLineStatusMonitor
+
+logging.basicConfig(level=logging.DEBUG,
+                    format='%(asctime)s %(levelname)-8s %(message)s',
+                    datefmt='%a, %d %b %Y %H:%M:%S',
+                    #filename='pipeline_main.log',
+                    filemode='w')
 
 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/'