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 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,
                          }

diff --git a/htsworkflow/templates/qseq.condor b/htsworkflow/templates/qseq.condor
index fcdac83778c04e60846212a9ce2a8ee7fde1cd76..68d101b78eca55284179a8c45b2d437f3a12da52 100644 (file)
--- 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 3ea03509b9de3b8073784584b11dff23c18aea92..127a9c0122edd4351728d62c4b85d129c617bc26 100644 (file)
--- 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 1c8e8547e02d7137a2898045648d1dc354e55d26..4428529ffde117f9649587ef854d33c64d4ea8b3 100644 (file)
--- 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 %}"