mark the example submission rule files as being raw, so the escapes dont get confused

[htsworkflow.git] / encode_submission / ucsc_gather.py

diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index c45e3820bbc8b9f146684bef9ed8f5443fb03f8e..a9fa72a83ddc1c4263e509070f50053d238fa405 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, \
@@ -93,7 +96,8 @@ def main(cmdline=None):
         mapper.link_daf(results)
 
     if opts.fastq:
-        extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
+        flowcells = os.path.join(opts.sequence, 'flowcells')
+        extractor = CondorFastqExtract(opts.host, flowcells,
                                        force=opts.force)
         extractor.create_scripts(results)