Fix some mismatches between variable names in python code and in templates

[htsworkflow.git] / htsworkflow / submission / condorfastq.py

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 1d425ded8458450967d1a2f22e0f63fc95337a95..64eb6a1892a93ab086adb377552db4a828a2a974 100644 (file)
--- a/htsworkflow/submission/condorfastq.py
+++ b/htsworkflow/submission/condorfastq.py
@@ -51,12 +51,16 @@ class CondorFastqExtract(object):
                         'by_sample': 'lane_to_fastq.turtle',
                         }
 
+        env = None
+        pythonpath = os.environ.get('PYTHONPATH', None)
+        if pythonpath is not None:
+            env = "PYTHONPATH=%s" % (pythonpath,)
         condor_entries = self.build_condor_arguments(result_map)
         for script_type in template_map.keys():
             template = loader.get_template(template_map[script_type])
             variables = {'python': sys.executable,
                          'logdir': self.log_path,
-                         'env': os.environ.get('PYTHONPATH', None),
+                         'env': env,
                          'args': condor_entries[script_type],
                          'root_url': self.api.root_url,
                          }