Always include the python path when generating the condor scripts

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 43e45548dfba9d0892ac528be200a55edfd0dfce..a0d0f1dedc0dd82c829447eab03e61ede3d8b0ed 100644 (file)
--- a/htsworkflow/submission/condorfastq.py
+++ b/htsworkflow/submission/condorfastq.py
@@ -90,9 +90,12 @@ executable=%(exe)s
 error=%(log)s/fastq.$(process).out
 output=%(log)s/fastq.$(process).out
 log=%(log)s/fastq.log
+environment="PYTHONPATH=%(env)s"
 
 """ % {'exe': sys.executable,
-       'log': self.log_path }
+       'log': self.log_path,
+       'env': os.environ.get('PYTHONPATH', '')
+      }
 
     def get_qseq_condor_header(self):
         return """Universe=vanilla
@@ -100,9 +103,12 @@ executable=%(exe)s
 error=%(log)s/qseq2fastq.$(process).out
 output=%(log)s/qseq2fastq.$(process).out
 log=%(log)s/qseq2fastq.log
+environment="PYTHONPATH=%(env)s"
 
 """ % {'exe': sys.executable,
-       'log': self.log_path }
+       'log': self.log_path,
+       'env': os.environ.get('PYTHONPATH','')
+      }
 
     def get_srf_condor_header(self):
         return """Universe=vanilla