From: Diane Trout <diane@caltech.edu>
Date: Thu, 9 Aug 2012 19:53:32 +0000 (-0700)
Subject: Fix some mismatches between variable names in python code and in templates
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=a17e7f21fbc053ea773f1ecefc0505f1dd1aec19

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

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 1d425de..64eb6a1 100644
--- 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,
                          }
diff --git a/htsworkflow/templates/qseq.condor b/htsworkflow/templates/qseq.condor
index fcdac83..68d101b 100644
--- a/htsworkflow/templates/qseq.condor
+++ b/htsworkflow/templates/qseq.condor
@@ -1,9 +1,9 @@
 Universe=vanilla
-executable={{ exe }}
+executable={{ python }}
 error={{ logdir }}/fastq.$(process).out
 output={{ logdir }}/fastq.$(process).out
 log={{ logdir }}/fastq.log
-{% if env %}environment={{ env }}{% endif %}
+{% if env %}environment="{{env}}"{% endif %}
 
 {% for arg in args %}
 arguments="{{ arg.pyscript }} -o {{ arg.target }} {% if arg.flowcell %}-f {{ arg.flowcell }}{% endif %} {% if arg.istar %}-i{% endif %} {% for s in arg.sources %}{{ s }} {% endfor %}"
diff --git a/htsworkflow/templates/split_fastq.condor b/htsworkflow/templates/split_fastq.condor
index 3ea0350..127a9c0 100644
--- a/htsworkflow/templates/split_fastq.condor
+++ b/htsworkflow/templates/split_fastq.condor
@@ -1,11 +1,11 @@
 Universe=vanilla
-executable={{ exe }}
+executable={{ python }}
 error={{ logdir }}/fastq.$(process).out
 output={{ logdir }}/fastq.$(process).out
 log={{ logdir }}/fastq.log
-{% if env %}environment={{ env }}{% endif %}
+{% if env %}environment="{{env}}"{% endif %}
 
 {% for arg in args %}
-arguments="{{ arg.pyscript }} -o {{ arg.target }} {% for s in arg.sources %}{{ s }} {% endfor %}
+arguments="{{ arg.pyscript }} -o {{ arg.target }} {% for s in arg.sources %}{{ s }} {% endfor %}"
 queue
 {% endfor %}
diff --git a/htsworkflow/templates/srf.condor b/htsworkflow/templates/srf.condor
index 1c8e854..4428529 100644
--- a/htsworkflow/templates/srf.condor
+++ b/htsworkflow/templates/srf.condor
@@ -1,9 +1,9 @@
 Universe=vanilla
-executable={{ exe }}
+executable={{ python }}
 error={{ logdir }}/fastq.$(process).out
 output={{ logdir }}/fastq.$(process).out
 log={{ logdir }}/fastq.log
-{% if env %}environment={{ env }}{% endif %}
+{% if env %}environment="{{env}}"{% endif %}
 
 {% for arg in args %}
 arguments="{{ arg.pyscript }}  {{ arg.sources.0 }} --verbose {% if arg.flowcell %}--flowcell {{ arg.flowcell }}{% endif %} {% if arg.ispaired %}--left {{ arg.target }} --right {{ arg.target_right }}{% else %}--single {{ arg.target }}{% endif %}"