diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 4759fa8f1b4..be0577f90ae 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -768,6 +768,7 @@ class JobWrapper( object ):
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination( from_job=job )
 
+        self.__commands_in_new_shell = self.app.config.commands_in_new_shell
         self.__user_system_pwent = None
         self.__galaxy_system_pwent = None
 
@@ -793,9 +794,15 @@ class JobWrapper( object ):
     def shell(self):
         return self.job_destination.shell or getattr(self.app.config, 'default_job_shell', DEFAULT_JOB_SHELL)
 
+    def disable_commands_in_new_shell(self):
+        """Provide an extension point to disable this isolation,
+        Pulsar builds its own job script so this is not needed for
+        remote jobs."""
+        self.__commands_in_new_shell = False
+
     @property
     def commands_in_new_shell(self):
-        return self.app.config.commands_in_new_shell
+        return self.__commands_in_new_shell
 
     @property
     def galaxy_lib_dir(self):
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 62a1557d99c..6b33adc8deb 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -278,6 +278,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
                 compute_tool_directory=remote_tool_directory,
                 compute_job_directory=remote_job_directory,
             )
+            job_wrapper.disable_commands_in_new_shell()
             command_line = build_command(
                 self,
                 job_wrapper=job_wrapper,