From 747b1cc1a4394028eb4996c4a314bc5f66cc12fe Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 18 Dec 2008 23:43:38 +0000
Subject: [PATCH] rename config file to something that doesn't include the read
 length since that has been changing.

also a minor code clean up.
---
 htsworkflow/automation/runner.py       | 2 +-
 htsworkflow/pipelines/configure_run.py | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/htsworkflow/automation/runner.py b/htsworkflow/automation/runner.py
index 21514c1..0ab2217 100644
--- a/htsworkflow/automation/runner.py
+++ b/htsworkflow/automation/runner.py
@@ -160,7 +160,7 @@ class Runner(rpc.XmlRpcBot):
 
         # retrieve config step
         cfg_filepath = os.path.join(conf_info.analysis_dir,
-                                    'config32auto.txt')
+                                    'config-auto.txt')
         status_retrieve_cfg = retrieve_config(conf_info,
                                           flowcell,
                                           cfg_filepath,
diff --git a/htsworkflow/pipelines/configure_run.py b/htsworkflow/pipelines/configure_run.py
index 0c1dc8b..54677b8 100644
--- a/htsworkflow/pipelines/configure_run.py
+++ b/htsworkflow/pipelines/configure_run.py
@@ -447,12 +447,11 @@ def configure(conf_info):
   ferr = open(stderr_filepath, 'w')
   
   pipe = subprocess.Popen(['goat_pipeline.py',
-                    '--GERALD=%s' % (conf_info.config_filepath),
-                           #'--tiles=s_4_0100,s_4_0101,s_4_0102,s_4_0103,s_4_0104',
+                           '--GERALD=%s' % (conf_info.config_filepath),
                            '--make',
                            conf_info.analysis_dir],
-                          stdout=fout,
-                          stderr=ferr)
+                           stdout=fout,
+                           stderr=ferr)
 
   print "Configuring pipeline: %s" % (time.ctime())
   error_code = pipe.wait()
-- 
2.30.2