From 4182122ad1e29f73fe9b16031473baf5c2b569d8 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 7 Mar 2012 15:58:12 -0800 Subject: [PATCH] Always include the python path when generating the condor scripts --- htsworkflow/submission/condorfastq.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py index 43e4554..a0d0f1d 100644 --- 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 -- 2.30.2