Fixing ClusterExecutor not writing job arrays

EdinburghGenomics · Oct 27, 2016 · aff489c · aff489c
1 parent 082f0c7
commit aff489c
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/egcg_core/executor/cluster_executor.py b/egcg_core/executor/cluster_executor.py
@@ -25,14 +25,14 @@ def __init__(self, *cmds, prelim_cmds=None, **cluster_config):
 
     def write_script(self):
         if self.prelim_cmds:
-            self.writer.register_cmds(*self.prelim_cmds)
+            self.writer.register_cmds(*self.prelim_cmds, parallel=False)
 
         pre_job_source = cfg.query('executor', 'pre_job_source')
         if pre_job_source:
             self.writer.register_cmd('source ' + pre_job_source)
 
         self.writer.line_break()
-        self.writer.register_cmds(*self.cmds)
+        self.writer.register_cmds(*self.cmds, parallel=True)
         self.writer.add_header()
         self.writer.save()
 

diff --git a/egcg_core/executor/script_writers/script_writer.py b/egcg_core/executor/script_writers/script_writer.py
@@ -32,7 +32,7 @@ def register_cmd(self, cmd, log_file=None):
             cmd += ' > %s 2>&1' % log_file
         self.add_line(cmd)
 
-    def register_cmds(self, *cmds, parallel=False):
+    def register_cmds(self, *cmds, parallel):
         if parallel:
             self.add_job_array(*cmds)
         else:

diff --git a/tests/test_executor/test_script_writers.py b/tests/test_executor/test_script_writers.py
@@ -29,7 +29,7 @@ def test_register_cmd(self):
         assert self.script_writer.lines == ['a_cmd > a_log_file 2>&1']
 
     def test_register_cmds(self):
-        self.script_writer.register_cmds('this', 'that')
+        self.script_writer.register_cmds('this', 'that', parallel=False)
         assert self.script_writer.lines == ['this', 'that']
 
     def test_add_job_array(self):
@@ -96,7 +96,7 @@ def setUp(self):
 
     def test(self):
         self.script_writer.log_commands = False
-        self.script_writer.register_cmds('some', 'preliminary', 'cmds')
+        self.script_writer.register_cmds('some', 'preliminary', 'cmds', parallel=False)
         self.script_writer.register_cmds('this', 'that', 'other', parallel=True)
         self.script_writer.add_header()