Merge branch 'master' of gitosis@mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / scripts / configure_pipeline

diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline
deleted file mode 100644 (file)
index 0251337..0000000
--- a/scripts/configure_pipeline
+++ /dev/null
@@ -1,88 +0,0 @@
-#!/usr/bin/env python
-import os
-import sys
-import re
-from htsworkflow.pipelines.configure_run import *
-from htsworkflow.pipelines import retrieve_config as _rc
-from htsworkflow.pipelines.run_status import startCmdLineStatusMonitor
-
-s_fc = re.compile('FC[0-9]+')
-
-#Turn on built-in command-line parsing.
-_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
-  if len(args) == 1:
-    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:
-    print "usage:\n" \
-          "       configure_pipeline FC#####\n" \
-          " or:\n" \
-          "       configure_pipeline <conf_filepath>\n"
-    return 3
-
-  genome_dir = GENOME_DIR
-
-  if not skip_retrieve_config:
-    status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
-    if status_retrieve_cfg:
-      print "Retrieve config file successful"
-    else:
-      print "Failed to retrieve config file"
-  else:
-    print "Config file %s provided from command-line" % (cfg_filepath)
-    ci.config_filepath = cfg_filepath
-    status_retrieve_cfg = True
-  
-  if status_retrieve_cfg:
-    status = configure(ci)
-    if status:
-      print "Configure success"
-    else:
-      print "Configure failed"
-    
-    print 'Run Dir:', ci.run_path
-    print 'Bustard Dir:', ci.bustard_path
-    
-    if status:
-      # Setup status cmdline status monitor
-      startCmdLineStatusMonitor(ci)
-      
-      print 'Running pipeline now!'
-      run_status = run_pipeline(ci)
-      if run_status is True:
-        print 'Pipeline ran successfully.'
-        return 0
-      else:
-        print 'Pipeline run failed.'
-        return 1
-
-    return 2
-
-if __name__ == "__main__":
-  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')
-
-  sys.exit(main(sys.argv[1:]))