[project @ Allow user to provide FC##### to download or a path to a config file.]

diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline
index d0d8b99af6cb36e37bedbb8eba746444e7220064..62ebb9b862192f2c79d0f797c25c3829a123c0f9 100644 (file)
--- a/scripts/configure_pipeline
+++ b/scripts/configure_pipeline
@@ -1,9 +1,16 @@
 #!/usr/bin/env python
 import os
 import sys
+import re
 from gaworkflow.pipeline.configure_run import *
 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
 
+s_fc = re.compile('FC[0-9]+')
+
+
+GENOME_DIR = '/data-store01/compbio/genomes/'
+
+
 
 def main(args=None):
   ci = ConfigInfo()
@@ -11,13 +18,24 @@ def main(args=None):
   #FIXME: make a better command line tool
   skip_retrieve_config = False
   if len(args) == 1:
-    cfg_filepath = os.path.abspath(args[0])
-    skip_retrieve_config = True
+    arg = args[0]
+
+    #If FC##### found
+    if s_fc.search(arg):
+      cfg_filepath = os.path.abspath('config32auto.txt')
+      flowcell = arg
+    #else, config file provide
+    else:
+      cfg_filepath = os.path.abspath(args[0])
+      skip_retrieve_config = True
   else:
-    cfg_filepath = os.path.abspath('config32auto.txt')
+    print "usage:\n" \
+          "       configure_pipeline FC#####\n" \
+          " or:\n" \
+          "       configure_pipeline <conf_filepath>\n"
+    return 3
 
-  flowcell = 'FC12150'
-  genome_dir = '/home/king/trog_drive/'
+  genome_dir = GENOME_DIR
 
   if not skip_retrieve_config:
     status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)