From 75ebecaffdedcfd1433cf48d545a2353ba44b38f Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Fri, 27 Jul 2012 15:35:00 -0700 Subject: [PATCH] Fix issues introduced when switching to the django templating system for fastq generation. It needs to know where django is, and I didn't include a short form for identifying flowcells. --- encode_submission/ucsc_gather.py | 3 +++ htsworkflow/templates/srf.condor | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py index c45e382..811ffdf 100644 --- 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 21d5232..1c8e854 100644 --- 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 %} -- 2.30.2