Fix issues introduced when switching to the django templating system for fastq genera...

It needs to know where django is, and I didn't include a short form for
identifying flowcells.

diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index c45e3820bbc8b9f146684bef9ed8f5443fb03f8e..811ffdfc277373e86b6f0f3fe7f9782463c8bdb0 100644 (file)
--- a/encode_submission/ucsc_gather.py
+++ b/encode_submission/ucsc_gather.py
@@ -21,6 +21,9 @@ from zipfile import ZipFile
 
 import RDF
 
+if not 'DJANGO_SETTINGS_MODULE' in os.environ:
+    os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
+
 from htsworkflow.util import api
 from htsworkflow.util.rdfhelp import \
      dafTermOntology, \

diff --git a/htsworkflow/templates/srf.condor b/htsworkflow/templates/srf.condor
index 21d523258e2028dbccad2785ad7a51e8b66dd5e9..1c8e8547e02d7137a2898045648d1dc354e55d26 100644 (file)
--- a/htsworkflow/templates/srf.condor
+++ b/htsworkflow/templates/srf.condor
@@ -6,6 +6,6 @@ log={{ logdir }}/fastq.log
 {% if env %}environment={{ env }}{% endif %}
 
 {% for arg in args %}
-arguments="{{ arg.pyscript }}  {{ arg.sources.0 }} --verbose {% if arg.flowcell %}-f {{ arg.flowcell }}{% endif %} {% if arg.ispaired %}--left {{ arg.target }} --right {{ arg.target_right }}{% else %}--single {{ arg.target }}{% endif %}"
+arguments="{{ arg.pyscript }}  {{ arg.sources.0 }} --verbose {% if arg.flowcell %}--flowcell {{ arg.flowcell }}{% endif %} {% if arg.ispaired %}--left {{ arg.target }} --right {{ arg.target_right }}{% else %}--single {{ arg.target }}{% endif %}"
 queue
 {% endfor %}