Work towards disabling command-line parsing outside of use

[htsworkflow.git] / scripts / configure_pipeline

diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline
index 62ebb9b862192f2c79d0f797c25c3829a123c0f9..b5126047a4e00f56d66f62abedff1097471a88c4 100644 (file)
--- a/scripts/configure_pipeline
+++ b/scripts/configure_pipeline
@@ -3,10 +3,13 @@ import os
 import sys
 import re
 from gaworkflow.pipeline.configure_run import *
+from gaworkflow.pipeline import retrieve_config
 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
 
 GENOME_DIR = '/data-store01/compbio/genomes/'