Introduces additional parameter to avoid having the command-line modi…

…fied for kubernetes.

lib/galaxy/jobs/command_factory.py

@@ -20,6 +20,7 @@ def build_command(
     runner,
     job_wrapper,
     container=None,
+    modify_command_for_container=True,
     include_metadata=False,
     include_work_dir_outputs=True,
     create_tool_working_directory=True,
@@ -57,14 +58,14 @@ def build_command(
     if not container:
         __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)
 
-    if container or job_wrapper.commands_in_new_shell:
-        if container:
+    if (container and modify_command_for_container) or job_wrapper.commands_in_new_shell:
+        if container and modify_command_for_container:
             # Many Docker containers do not have /bin/bash.
             external_command_shell = "/bin/sh"
         else:
             external_command_shell = shell
         externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params)
-        if container:
+        if container and modify_command_for_container:
             # Stop now and build command before handling metadata and copying
             # working directory files back. These should always happen outside
             # of docker container - no security implications when generating

lib/galaxy/jobs/runners/__init__.py

@@ -145,7 +145,8 @@ def parse_destination_params(self, params):
         """
         raise NotImplementedError()
 
-    def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True):
+    def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
+                    modify_command_for_container=True):
         """Some sanity checks that all runners' queue_job() methods are likely to want to do
         """
         job_id = job_wrapper.get_id_tag()
@@ -171,6 +172,7 @@ def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outp
                 job_wrapper,
                 include_metadata=include_metadata,
                 include_work_dir_outputs=include_work_dir_outputs,
+                modify_command_for_container=modify_command_for_container
             )
         except Exception as e:
             log.exception("(%s) Failure preparing job" % job_id)
@@ -193,13 +195,15 @@ def stop_job(self, job):
     def recover(self, job, job_wrapper):
         raise NotImplementedError()
 
-    def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ):
+    def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
+                            modify_command_for_container=True ):
         container = self._find_container( job_wrapper )
         return build_command(
             self,
             job_wrapper,
             include_metadata=include_metadata,
             include_work_dir_outputs=include_work_dir_outputs,
+            modify_command_for_container=modify_command_for_container,
             container=container
         )
 

lib/galaxy/jobs/runners/kubernetes.py

@@ -64,7 +64,9 @@ def queue_job(self, job_wrapper):
         # prepare the job
         # We currently don't need to include_metadata or include_work_dir_outputs, as working directory is the same
         # were galaxy will expect results.
-        if not self.prepare_job(job_wrapper, include_metadata=False, include_work_dir_outputs=False):
+        log.debug("Starting queue_job for job " + job_wrapper.get_id_tag())
+        if not self.prepare_job(job_wrapper, include_metadata=False, include_work_dir_outputs=False,
+                                modify_command_for_container=False):
             return
 
         job_destination = job_wrapper.job_destination