Set WITH_SEQUENCE as both a per-lane AND global parameter

[htsworkflow.git] / htsworkflow / pipelines / retrieve_config.py

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index f9d4e3ba0df83a4b918a5fafcdc5e5cded75c117..3a1a56aeaf2188350db8b980d7b098bf0098a0ba 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -14,6 +14,7 @@ except ImportError, e:
     import simplejson as json
 
 from htsworkflow.frontend.auth import apidata
+from htsworkflow.util import api
 from htsworkflow.util.url import normalize_url
 from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
 from htsworkflow.pipelines.genome_mapper import constructMapperDict
@@ -36,7 +37,7 @@ def retrieve_flowcell_info(base_host_url, flowcell):
     """
     Return a dictionary describing a 
     """
-    url = base_host_url + '/experiments/config/%s/json' % (flowcell)
+    url = api.flowcell_url(base_host_url, flowcell)
   
     try:
         apipayload = urllib.urlencode(apidata)
@@ -107,7 +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)
 
@@ -123,6 +123,10 @@ 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 += ['WITH_SEQUENCE TRUE']
+    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)
@@ -140,7 +144,7 @@ def format_gerald_config(options, flowcell_info, genome_map):
             is_sequencing = True
             
         if is_sequencing:
-            config += ['%s:ANALYSIS sequence%s' % (lane_prefix, analysis_suffix)]
+            config += ['%s:ANALYSIS sequence%s' % (lane_prefix, sequence_suffix)]
         else:
             config += ['%s:ANALYSIS eland%s' % (lane_prefix, analysis_suffix)]
             config += ['%s:ELAND_GENOME %s' % (lane_prefix, species_path) ]