diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 7d94947a921..306ab63e97e 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -117,6 +117,83 @@
           -->
           <!-- <param id="pulsar_config">path/to/pulsar/app.yml</param> -->
         </plugin>
+        <plugin id="k8s" type="runner" load="galaxy.jobs.runners.kubernetes:kubernetes">
+            <!-- The Kubernetes (k8s) plugin allows to send jobs to a k8s cluster which shares filesystem with Galaxy.
+                 The shared file system needs to be exposed to k8s through a Persistent Volume (rw) and a Persistent
+                 Volume Claim. An example of a Persistent Volume could be, in yaml (access modes, reclaim policy and
+                 path are relevant) (persistent_volume.yaml):
+
+                    kind: PersistentVolume
+                    apiVersion: v1
+                    metadata:
+                      name: pv-galaxy-nfs
+                      labels:
+                        type: nfs
+                    spec:
+                      capacity:
+                        storage: 10Gi
+                      accessModes:
+                        - ReadWriteMany
+                      persistentVolumeReclaimPolicy: Retained
+                      nfs:
+                        path: /scratch1/galaxy_data
+                        server: 192.168.64.1
+
+                 The path (nfs:path: in the example) set needs to be a parent directory of the directories used for
+                 variables “file_path” and “new_file_path” on the galaxy.ini files. Clearly, for this particular example
+                 to work, there needs to be a NFS server serving that directory on that ip. Please make sure that you
+                 use reasonable storage size for your set up (possibly larger that the 10Gi written).
+                 An example of the volume claim should be (this needs to be followed more closely) (pv_claim.yaml):
+
+                    kind: PersistentVolumeClaim
+                    apiVersion: v1
+                    metadata:
+                      name: galaxy-pvc
+                    spec:
+                      accessModes:
+                        - ReadWriteMany
+                      volumeName: pv-galaxy-nfs
+                      resources:
+                        requests:
+                          storage: 2Gi
+
+                 The volume claim needs to reference the name of the volume in spec:volumeName. The name of the claim
+                 (metadat:name) is referenced in the plugin definition (see below), through param
+                 "k8s_persistent_volume_claim_name". These two k8s object need to be created before galaxy can use them:
+
+                 kubectl create -f <path/to/persistent_volume.yaml>
+                 kubectl create -f <path/to/pv_claim.yaml>
+
+                 pointing of course to the same Kubernetes cluster that you intend to use.
+            -->
+
+            <param id="k8s_config_path">/path/to/kubeconfig</param>
+            <!--- This is the path to the kube config file, which is normally on ~/.kube/config, but that will depend on
+                 your installation. This is the file that tells the plugin where the k8s cluster is, access credentials,
+                 etc. -->
+
+            <param id="k8s_persistent_volume_claim_name">galaxy_pvc</param>
+            <!-- The name of the Persisten Volume Claim (PVC) to be used, details above, needs to match the PVC's
+                 metadata:name -->
+
+            <param id="k8s_persistent_volume_claim_mount_path">/scratch1/galaxy_data</param>
+            <!-- The mount path needs to be parent directory of the "file_path" and "new_file_path" paths
+                 set in universe_wsgi.ini (or equivalent general galaxy config file). This is the mount path of the
+                 PVC within the docker container that will be actually running the tool -->
+
+            <param id="k8s_namespace">galaxy-instanceA</param>
+            <!-- The namespace to be used on the Kubernetes cluster, if different from default, this needs to be set
+                 accordingly in the PV and PVC detailed above -->
+
+            <param id="k8s_pod_retrials">4</param>
+            <!-- Allows pods to retry up to this number of times, before marking the galaxy job failed. k8s is a state
+                 setter essentially, so by default it will try to take a job submitted to successful completion. A job
+                 submits pods, until the number of successes (1 in this use case) is achieved, assuming that whatever is
+                 making the pods fail will be fixed (such as a stale disk or a dead node that it is being restarted).
+                 This option sets a limit of retrials, so that after that number of failed pods, the job is re-scaled to
+                 zero (no execution) and the stderr/stdout of the k8s job is reported in galaxy (and the galaxy job set
+                 to failed) -->
+        </plugin>
 
     </plugins>
     <handlers default="handlers">
@@ -495,6 +572,61 @@
             <param id="docker_enabled" from_config="use_docker">false</param>
         </destination>
 
+        <destination id="my-tool-container" runner="k8s">
+            <!-- For the kubernetes (k8s) runner, each container is a destination.
+
+                 Make sure that the container is able to execute the calls that will be passed by the galaxy built
+                 command. Most notably, containers that execute scripts through an interpreter in the form
+                 Rscript my-script.R <arguments>
+                 should have this wrapped as the container set working directory won't be the one actually used by
+                 galaxy (galaxy creates a new working director and moves to it). Recommendation is hence to wrap this
+                 type of calls on a shell script, and leave that script with execution privileges on the PATH of the
+                 container:
+
+                 RUN echo '#!/bin/bash' > /usr/local/bin/myScriptExec
+                 RUN echo 'Rscript /path/to/my-script.r "$@"' >> /usr/local/bin/myScriptExec
+                 RUN chmod a+x /usr/local/bin/myScriptExec
+
+            -->
+
+            <!-- The following four fields assemble the container's full name:
+                 docker pull <repo>/<owner>/<image>:tag
+            -->
+            <param id="docker_repo_override">my-docker-registry.org</param>
+            <param id="docker_owner_override">superbioinfo</param>
+            <param id="docker_image_override">my-tool</param>
+            <param id="docker_tag_override">latest</param>
+            <!-- Alternatively you could specify a different type of container, such as rkt (not tested with Kubernetes)
+                <param id="rkt_repo_override">my-docker-registry.org</param>
+                <param id="rkt_owner_override">superbioinfo</param>
+                <param id="rkt_image_override">my-tool</param>
+                <param id="rkt_tag_override">latest</param>
+            -->
+            <!-- You can also allow the destination to accept the docker container set in the tool, and only fall into
+                 the docker image set by this destination if the tool doesn't set a docker container, by using the
+                 "default" suffix instead of "override".
+                <param id="docker_repo_default">my-docker-registry.org</param>
+                <param id="docker_owner_default">superbioinfo</param>
+                <param id="docker_image_default">my-tool</param>
+                <param id="docker_tag_default">latest</param>
+            -->
+            <param id="max_pod_retrials">3</param>
+            <!-- Allows pods to retry up to this number of times, before marking the galaxy job failed. k8s is a state
+                 setter essentially, so by default it will try to take a job submitted to successful completion. A job
+                 submits pods, until the number of successes (1 in this use case) is achieved, assuming that whatever is
+                 making the pods fail will be fixed (such as a stale disk or a dead node that it is being restarted).
+                 This option sets a limit of retrials, so that after that number of failed pods, the job is re-scaled to
+                 zero (no execution) and the stderr/stdout of the k8s job is reported in galaxy (and the galaxy job set
+                 to failed).
+
+                 Overrides the runner config. (Not implemented yet)
+            -->
+            <!-- REQUIRED: To play nicely with the existing galaxy setup for containers. This could be set though
+                 internally by the runner. -->
+            <param id="docker_enabled">true</param>
+        </destination>
+
+
         <!-- Templatized destinations - macros can be used to create templated
         destinations with reduced XML duplication. Here we are creating 4 destinations in 4 lines instead of 28 using the macros defined below.
         -->
@@ -526,6 +658,11 @@
              and pass to dynamic destination (as resource_params argument). -->
         <tool id="longbar" destination="dynamic" resources="all" />
         <tool id="baz" handler="special_handlers" destination="bigmem"/>
+
+        <!-- Finally for Kubernetes runner, the following connects a particular tool to be executed with
+             the container of choice in Kubernetes.
+        -->
+        <tool id="my-tool" destination="my-tool-container"/>
     </tools>
     <limits>
         <!-- Certain limits can be defined. The 'concurrent_jobs' limits all
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 728f2526a87..457f9eb6a6f 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -67,3 +67,7 @@ ecdsa==0.13
 
 # Flexible BAM index naming
 pysam==0.8.4+gx1
+
+# Kubernetes runner pykube requirement
+-e git+https://github.com/pcm32/pykube.git@feature/allMergedFeatures#egg=pykube
+
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index 62b5384088f..2bdbb2052f3 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/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
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index d129d46e3b7..9861afc4f10 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -145,7 +145,8 @@ class BaseJobRunner( object ):
         """
         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 @@ class BaseJobRunner( object ):
                 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 @@ class BaseJobRunner( object ):
     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
         )
 
diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
new file mode 100644
index 00000000000..3829ed8da7f
--- /dev/null
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -0,0 +1,311 @@
+"""
+Offload jobs to a Kubernetes cluster.
+"""
+
+import logging
+
+from galaxy import model
+from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner
+from os import environ as os_environ
+
+# pykube imports:
+try:
+    import operator
+
+    from pykube.config import KubeConfig
+    from pykube.http import HTTPClient
+    from pykube.objects import Job
+    from pykube.objects import Pod
+except ImportError as exc:
+    operator = None
+    K8S_IMPORT_MESSAGE = ('The Python pykube package is required to use '
+                          'this feature, please install it or correct the '
+                          'following error:\nImportError %s' % str(exc))
+
+log = logging.getLogger(__name__)
+
+__all__ = ['KubernetesJobRunner']
+
+
+class KubernetesJobRunner(AsynchronousJobRunner):
+    """
+    Job runner backed by a finite pool of worker threads. FIFO scheduling
+    """
+    runner_name = "KubernetesRunner"
+
+    def __init__(self, app, nworkers, **kwargs):
+        # Check if pykube was importable, fail if not
+        assert operator is not None, K8S_IMPORT_MESSAGE
+        runner_param_specs = dict(
+            k8s_config_path=dict(map=str, default=os_environ.get('KUBECONFIG', None)),
+            k8s_persistent_volume_claim_name=dict(map=str),
+            k8s_persistent_volume_claim_mount_path=dict(map=str),
+            k8s_namespace=dict(map=str, default="default"),
+            k8s_pod_retrials=dict(map=int, valid=lambda x: int > 0, default=3))
+
+        if 'runner_param_specs' not in kwargs:
+            kwargs['runner_param_specs'] = dict()
+        kwargs['runner_param_specs'].update(runner_param_specs)
+
+        """Start the job runner parent object """
+        super(KubernetesJobRunner, self).__init__(app, nworkers, **kwargs)
+
+        # self.cli_interface = CliInterface()
+
+        # here we need to fetch the default kubeconfig path from the plugin defined in job_conf...
+        self._pykube_api = HTTPClient(KubeConfig.from_file(self.runner_params["k8s_config_path"]))
+        self._galaxy_vol_name = "pvc-galaxy"  # TODO this needs to be read from params!!
+
+        self._init_monitor_thread()
+        self._init_worker_threads()
+
+    def queue_job(self, job_wrapper):
+        """Create job script and submit it to Kubernetes cluster"""
+        # 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.
+        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
+
+        # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/
+        k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper)
+        k8s_job_obj = {
+            "apiVersion": "extensions/v1beta1",
+            "kind": "Job",
+            "metadata":
+            # metadata.name is the name of the pod resource created, and must be unique
+            # http://kubernetes.io/docs/user-guide/configuring-containers/
+                {
+                    "name": k8s_job_name,
+                    "namespace": "default",  # TODO this should be set
+                    "labels": {"app": k8s_job_name},
+                }
+            ,
+            "spec": self.__get_k8s_job_spec(job_wrapper)
+        }
+
+        # Creates the Kubernetes Job
+        Job(self._pykube_api, k8s_job_obj).create()
+
+        # define job attributes in the AsyncronousJobState for follow-up
+        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper,
+                                   job_id=k8s_job_name, job_destination=job_destination)
+        self.monitor_queue.put(ajs)
+
+        # external_runJob_script can be None, in which case it's not used.
+        external_runjob_script = None
+        return external_runjob_script
+
+    def __produce_unique_k8s_job_name(self, job_wrapper):
+        # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
+        return "galaxy-" + job_wrapper.get_id_tag()
+
+    def __get_k8s_job_spec(self, job_wrapper):
+        """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template."""
+        k8s_job_spec = {"template": self.__get_k8s_job_spec_template(job_wrapper)}
+        return k8s_job_spec
+
+    def __get_k8s_job_spec_template(self, job_wrapper):
+        """The k8s spec template is nothing but a Pod spec, except that it is nested and does not have an apiversion
+        nor kind. In addition to required fields for a Pod, a pod template in a job must specify appropriate labels
+        (see pod selector) and an appropriate restart policy."""
+        k8s_spec_template = {
+            "metadata": {
+                "labels": {"app": self.__produce_unique_k8s_job_name(job_wrapper)}
+            },
+            "spec": {
+                "volumes": self.__get_k8s_mountable_volumes(job_wrapper),
+                "restartPolicy": self.__get_k8s_restart_policy(job_wrapper),
+                "containers": self.__get_k8s_containers(job_wrapper)
+            }
+        }
+        # TODO include other relevant elements that people might want to use from
+        # TODO http://kubernetes.io/docs/api-reference/v1/definitions/#_v1_podspec
+
+        return k8s_spec_template
+
+    def __get_k8s_restart_policy(self, job_wrapper):
+        """The default Kubernetes restart policy for Jobs"""
+        return "Never"
+
+    def __get_k8s_mountable_volumes(self, job_wrapper):
+        """Provides the required volumes that the containers in the pod should be able to mount. This should be using
+        the new persistent volumes and persistent volumes claim objects. This requires that both a PersistentVolume and
+        a PersistentVolumeClaim are created before starting galaxy (starting a k8s job).
+        """
+        # TODO on this initial version we only support a single volume to be mounted.
+        k8s_mountable_volume = {
+            "name": self._galaxy_vol_name,
+            "persistentVolumeClaim": {
+                "claimName": self.runner_params['k8s_persistent_volume_claim_name']
+            }
+        }
+        return [k8s_mountable_volume]
+
+    def __get_k8s_containers(self, job_wrapper):
+        """Fills in all required for setting up the docker containers to be used."""
+        k8s_container = {
+            "name": self.__get_k8s_container_name(job_wrapper),
+            "image": self._find_container(job_wrapper).container_id,
+            # 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
+            }]
+        }
+
+        # if self.__requires_ports(job_wrapper):
+        #    k8s_container['ports'] = self.__get_k8s_containers_ports(job_wrapper)
+
+        return [k8s_container]
+
+    # def __get_k8s_containers_ports(self, job_wrapper):
+
+    #    for k,v self.runner_params:
+    #        if k.startswith("container_port_"):
+
+    def __assemble_k8s_container_image_name(self, job_wrapper):
+        """Assembles the container image name as repo/owner/image:tag, where repo, owner and tag are optional"""
+        job_destination = job_wrapper.job_destination
+
+        # Determine the job's Kubernetes destination (context, namespace) and options from the job destination
+        # definition
+        repo = ""
+        owner = ""
+        if 'repo' in job_destination.params:
+            repo = job_destination.params['repo'] + "/"
+        if 'owner' in job_destination.params:
+            owner = job_destination.params['owner'] + "/"
+
+        k8s_cont_image = repo + owner + job_destination.params['image']
+
+        if 'tag' in job_destination.params:
+            k8s_cont_image += ":" + job_destination.params['tag']
+
+        return k8s_cont_image
+
+    def __get_k8s_container_name(self, job_wrapper):
+        # TODO check if this is correct
+        return job_wrapper.job_destination.id
+
+    def check_watched_item(self, job_state):
+        """Checks the state of a job already submitted on k8s. Job state is a AsynchronousJobState"""
+        jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id)
+        if len(jobs.response['items']) == 1:
+            job = Job(self._pykube_api, jobs.response['items'][0])
+            succeeded = 0
+            active = 0
+            failed = 0
+            if 'succeeded' in job.obj['status']:
+                succeeded = job.obj['status']['succeeded']
+            if 'active' in job.obj['status']:
+                active = job.obj['status']['active']
+            if 'failed' in job.obj['status']:
+                failed = job.obj['status']['failed']
+
+            # This assumes jobs dependent on a single pod, single container
+            if succeeded > 0:
+                self.__produce_log_file(job_state)
+                error_file = open(job_state.error_file, 'w')
+                error_file.write("")
+                error_file.close()
+                job_state.running = False
+                self.mark_as_finished(job_state)
+                return None
+
+            elif active > 0 or succeeded + active + failed == 0:
+                job_state.running = True
+                return job_state
+            elif failed > job_state.job_destination.params['max_pod_retrials']:
+                self.__produce_log_file(job_state)
+                error_file = open(job_state.error_file, 'w')
+                error_file.write("Exceeded max number of Kubernetes pod retrials allowed for job\n")
+                error_file.close()
+                job_state.running = False
+                self.mark_as_failed(job_state)
+                job.scale(replicas=0)
+                return None
+
+            # We should not get here
+            log.debug(
+                "Reaching unexpected point for Kubernetes job, where it is not classified as succ., active nor failed.")
+            return job_state
+
+        elif len(jobs.response['items']) == 0:
+            # there is no job responding to this job_id, it is either lost or something happened.
+            log.error("No Jobs are available under expected selector app=" + job_state.job_id)
+            error_file = open(job_state.error_file, 'w')
+            error_file.write("No Kubernetes Jobs are available under expected selector app=" + job_state.job_id + "\n")
+            error_file.close()
+            self.mark_as_failed(job_state)
+            return job_state
+        else:
+            # there is more than one job associated to the expected unique job id used as selector.
+            log.error("There is more than one Kubernetes Job associated to job id " + job_state.job_id)
+            self.__produce_log_file(job_state)
+            error_file = open(job_state.error_file, 'w')
+            error_file.write("There is more than one Kubernetes Job associated to job id " + job_state.job_id + "\n")
+            error_file.close()
+            self.mark_as_failed(job_state)
+            return job_state
+
+    def __produce_log_file(self, job_state):
+        pod_r = Pod.objects(self._pykube_api).filter(selector="app=" + job_state.job_id)
+        logs = ""
+        for pod_obj in pod_r.response['items']:
+            pod = Pod(self._pykube_api, pod_obj)
+            logs += "\n\n==== Pod " + pod.name + " log start ====\n\n"
+            logs += pod.logs(timestamps=True)
+            logs += "\n\n==== Pod " + pod.name + " log end   ===="
+        logs_file_path = job_state.output_file
+        logs_file = open(logs_file_path, mode="w")
+        logs_file.write(logs)
+        logs_file.close()
+        return logs_file_path
+
+    def stop_job(self, job):
+        """Attempts to delete a dispatched job to the k8s cluster"""
+        try:
+            jobs = Job.objects(self._pykube_api).filter(selector="app=" + job.job_runner_external_id)
+            if jobs.response['items'].len() >= 0:
+                job_to_delete = Job(self._pykube_api, jobs.response['items'][0])
+                job_to_delete.scale(replicas=0)
+            # TODO assert whether job parallelism == 0
+            # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"
+            log.debug("(%s/%s) Terminated at user's request" % (job.id, job.job_runner_external_id))
+        except Exception as e:
+            log.debug("(%s/%s) User killed running job, but error encountered during termination: %s" % (
+                job.id, job.job_runner_external_id, e))
+
+    def recover(self, job, job_wrapper):
+        """Recovers jobs stuck in the queued/running state when Galaxy started"""
+        # TODO this needs to be implemented to override unimplemented base method
+        job_id = job.get_job_runner_external_id()
+        if job_id is None:
+            self.put(job_wrapper)
+            return
+        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
+        ajs.job_id = str(job_id)
+        ajs.command_line = job.command_line
+        ajs.job_wrapper = job_wrapper
+        ajs.job_destination = job_wrapper.job_destination
+        if job.state == model.Job.states.RUNNING:
+            log.debug("(%s/%s) is still in running state, adding to the runner monitor queue" % (
+                job.id, job.job_runner_external_id))
+            ajs.old_state = model.Job.states.RUNNING
+            ajs.running = True
+            self.monitor_queue.put(ajs)
+        elif job.state == model.Job.states.QUEUED:
+            log.debug("(%s/%s) is still in queued state, adding to the runner monitor queue" % (
+                job.id, job.job_runner_external_id))
+            ajs.old_state = model.Job.states.QUEUED
+            ajs.running = False
+            self.monitor_queue.put(ajs)
diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py
index 600234d6415..49f03220061 100644
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -102,7 +102,25 @@ class ContainerFinder(object):
     def __overridden_container_id(self, container_type, destination_info):
         if not self.__container_type_enabled(container_type, destination_info):
             return None
-        return destination_info.get("%s_container_id_override" % container_type)
+        if "%s_container_id_override" % container_type in destination_info:
+            return destination_info.get("%s_container_id_override" % container_type)
+        if "%s_image_override" % container_type in destination_info:
+            return self.__build_container_id_from_parts(container_type, destination_info, mode="override")
+
+    def __build_container_id_from_parts(self, container_type, destination_info, mode):
+        repo = ""
+        owner = ""
+        repo_key = "%s_repo_%s" % (container_type, mode)
+        owner_key = "%s_owner_%s" % (container_type, mode)
+        if repo_key in destination_info:
+            repo = destination_info[repo_key] + "/"
+        if owner_key in destination_info:
+            owner = destination_info[owner_key] + "/"
+        cont_id = repo + owner + destination_info["%s_image_%s" % (container_type, mode)]
+        tag_key = "%s_tag_%s" % (container_type, mode)
+        if tag_key in destination_info:
+            cont_id += ":" + destination_info[tag_key]
+        return cont_id
 
     def __default_container_id(self, container_type, destination_info):
         if not self.__container_type_enabled(container_type, destination_info):
@@ -111,7 +129,11 @@ class ContainerFinder(object):
         # Also allow docker_image...
         if key not in destination_info:
             key = "%s_image" % container_type
-        return destination_info.get(key)
+        if key in destination_info:
+            return destination_info.get(key)
+        elif "%s_image_default" in destination_info:
+            return self.__build_container_id_from_parts(container_type, destination_info, mode="default")
+        return None
 
     def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info):
         # TODO: ensure destination_info is dict-like