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Always include the python path when generating the condor scripts
author
Diane Trout
<diane@caltech.edu>
Wed, 7 Mar 2012 23:58:12 +0000
(15:58 -0800)
committer
Diane Trout
<diane@caltech.edu>
Wed, 7 Mar 2012 23:58:12 +0000
(15:58 -0800)
htsworkflow/submission/condorfastq.py
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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
error=%(log)s/fastq.$(process).out
output=%(log)s/fastq.$(process).out
log=%(log)s/fastq.log
+environment="PYTHONPATH=%(env)s"
""" % {'exe': sys.executable,
""" % {'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
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
error=%(log)s/qseq2fastq.$(process).out
output=%(log)s/qseq2fastq.$(process).out
log=%(log)s/qseq2fastq.log
+environment="PYTHONPATH=%(env)s"
""" % {'exe': sys.executable,
""" % {'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
def get_srf_condor_header(self):
return """Universe=vanilla