From: Diane Trout <diane@caltech.edu>
Date: Thu, 7 Oct 2010 22:32:45 +0000 (+0000)
Subject: Update gerald config file generation.
X-Git-Tag: 0.4.5~2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=a137f2ce607312b74c35647703c838a3c6a2c724

Update gerald config file generation.
Include ELAND_SET_SIZE, WITH_SEQUENCE options
Stop commenting SEQUENCE_FORMAT out
---

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index fbd1187..c3f32c7 100644
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -108,7 +108,6 @@ def format_gerald_header(flowcell_info):
         config += ['Lane%s: %s | %s' % (lane_number, lane_info['library_id'],
                                         lane_info['library_name'])]
 
-    config += ['SEQUENCE_FORMAT --fastq']
     config += ['']
     return "\n# ".join(config)
 
@@ -124,6 +123,9 @@ def format_gerald_config(options, flowcell_info, genome_map):
     # in the config file... things like which lane is which library.
     config = [format_gerald_header(flowcell_info)]
 
+    config += ['SEQUENCE_FORMAT --fastq']
+    config += ['ELAND_SET_SIZE 20']
+    config += ['12345678:WITH_SEQUENCE TRUE']
     analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
     sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
     lane_groups = group_lane_parameters(flowcell_info)
diff --git a/scripts/retrieve_config b/scripts/retrieve_config
old mode 100644
new mode 100755