Add a 'paired_end' flag to a flowcell.

Then use this flag in the eland_config module to specify ANALYSIS eland_pair
Also change the default analysis to eland_extended

use the following to add the new field
alter table fctracker_flowcell add column paired_end bool not null default false;

diff --git a/gaworkflow/frontend/eland_config/views.py b/gaworkflow/frontend/eland_config/views.py
index c4ff09732a8fb769d7f30d2ac56ddccd4ba15bf1..3eb2615224cc9dc71d96e9f995b4e1d66983fad0 100644 (file)
--- a/gaworkflow/frontend/eland_config/views.py
+++ b/gaworkflow/frontend/eland_config/views.py
@@ -346,7 +346,10 @@ def getElandConfig(flowcell, regenerate=False):
   #Loop through and create entries for each species.
   for genome in genome_list:
     lanes = ''.join(genome_dict[genome])
-    data.append('%s:ANALYSIS eland' % (lanes))
+    if fcObj.paired_end:
+        data.append('%s:ANALYSIS eland_pair' % (lanes))
+    else:
+        data.append('%s:ANALYSIS eland_extended' % (lanes))
     data.append('%s:READ_LENGTH %s' % (lanes, read_length))
     data.append('%s:ELAND_GENOME %s' % (lanes, '%%(%s)s' % (genome)))
     data.append('%s:USE_BASES %s' % (lanes, 'Y'*int(read_length)))

diff --git a/gaworkflow/frontend/fctracker/models.py b/gaworkflow/frontend/fctracker/models.py
index 8c2290709ccce7fd705896bb5940bd974dc902cb..46fcae177b63d28943228d828257a641d8158700 100644 (file)
--- a/gaworkflow/frontend/fctracker/models.py
+++ b/gaworkflow/frontend/fctracker/models.py
@@ -87,6 +87,7 @@ class FlowCell(models.Model):
   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
   run_date = models.DateTimeField(core=True)
   advanced_run = models.BooleanField(default=False)
+  paired_end = models.BooleanField(default=False)
   read_length = models.IntegerField(default=32)
   
   lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
@@ -132,7 +133,7 @@ class FlowCell(models.Model):
     list_display_links = ('run_date', 'flowcell_id', 'lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library')
     fields = (
         (None, {
-            'fields': ('run_date', 'flowcell_id', ('read_length', 'advanced_run'),)
+            'fields': ('run_date', 'flowcell_id', ('read_length', 'paired_end', 'advanced_run',),)
         }),
         ('Lanes:', {
             'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)