changes way that 'command' option is passed to k8s on the Job object …

…to cater for multi line commands.

lib/galaxy/jobs/runners/kubernetes.py

@@ -156,6 +156,11 @@ def __get_k8s_containers(self, job_wrapper):
         k8s_container = {
             "name": self.__get_k8s_container_name(job_wrapper),
             "image": self.__assemble_k8s_container_image_name(job_wrapper),
+            # this form of command overrides the entrypoint and allows multi command
+            # command line execution, separated by ;, which is what Galaxy does
+            # to assemble the command.
+            # TODO possibly shell needs to be set by job_wrapper
+            "command": "[\"/bin/bash\",\"-c\",\""+job_wrapper.runner_command_line+"\"]",
             "volumeMounts": {
                 "mountPath": self.runner_params['k8s_persistent_volume_claim_mount_path'],
                 "name": self._galaxy_vol_name