diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 9fca963bc962..7009eb1fe591 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -469,13 +469,20 @@ def __get_params(self, parent):
         rval = {}
         for param in parent.findall('param'):
             key = param.get('id')
-            param_value = param.text
+            if key in ["container", "container_override"]:
+                from galaxy.tools.deps import requirements
+                containers = map(requirements.container_from_element, list(param))
+                param_value = map(lambda c: c.to_dict(), containers)
+            else:
+                param_value = param.text
+
             if 'from_environ' in param.attrib:
                 environ_var = param.attrib['from_environ']
                 param_value = os.environ.get(environ_var, param_value)
             elif 'from_config' in param.attrib:
                 config_val = param.attrib['from_config']
                 param_value = self.app.config.config_dict.get(config_val, param_value)
+
             rval[key] = param_value
         return rval
 
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index 2c476a2bc524..f3fe7cc071fc 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -55,13 +55,13 @@ def build_command(
     # One could imagine also allowing dependencies inside of the container but
     # that is too sophisticated for a first crack at this - build your
     # containers ready to go!
-    if not container:
+    if not container or container.resolve_dependencies:
         __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)
 
     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"
+            external_command_shell = container.shell
         else:
             external_command_shell = shell
         externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params)
diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py
index 49f032200613..2cc824759efc 100644
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -9,6 +9,8 @@
 
 from galaxy.util import asbool
 from ..deps import docker_util
+from .requirements import ContainerDescription
+from .requirements import DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, DEFAULT_CONTAINER_SHELL
 
 import logging
 log = logging.getLogger(__name__)
@@ -55,10 +57,18 @@ def __destination_container(container_description=None, container_id=None, conta
                 container_type,
                 tool_info,
                 destination_info,
-                job_info
+                job_info,
+                container_description,
             )
             return container
 
+        if "container_override" in destination_info:
+            container_description = ContainerDescription.from_dict(destination_info["container_override"][0])
+            if container_description:
+                container = __destination_container(container_description)
+                if container:
+                    return container
+
         # Is destination forcing Galaxy to use a particular container do it,
         # this is likely kind of a corner case. For instance if deployers
         # do not trust the containers annotated in tools.
@@ -90,6 +100,13 @@ def __destination_container(container_description=None, container_id=None, conta
 
         # If we still don't have a container, check to see if any container
         # types define a default container id and use that.
+        if "container" in destination_info:
+            container_description = ContainerDescription.from_dict(destination_info["container"][0])
+            if container_description:
+                container = __destination_container(container_description)
+                if container:
+                    return container
+
         for container_type in CONTAINER_CLASSES.keys():
             container_id = self.__default_container_id(container_type, destination_info)
             if container_id:
@@ -135,7 +152,7 @@ def __default_container_id(self, container_type, 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):
+    def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info, container_description=None):
         # TODO: ensure destination_info is dict-like
         if not self.__container_type_enabled(container_type, destination_info):
             return NULL_CONTAINER
@@ -144,7 +161,7 @@ def __destination_container(self, container_id, container_type, tool_info, desti
         # container type is - there should be more thought put into this.
         # Checking which are availalbe - settings policies for what can be
         # auto-fetched, etc....
-        return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info)
+        return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info, container_description)
 
     def __container_type_enabled(self, container_type, destination_info):
         return asbool(destination_info.get("%s_enabled" % container_type, False))
@@ -208,12 +225,21 @@ def __init__(self, working_directory, tool_directory, job_directory):
 class Container( object ):
     __metaclass__ = ABCMeta
 
-    def __init__(self, container_id, app_info, tool_info, destination_info, job_info):
+    def __init__(self, container_id, app_info, tool_info, destination_info, job_info, container_description):
         self.container_id = container_id
         self.app_info = app_info
         self.tool_info = tool_info
         self.destination_info = destination_info
         self.job_info = job_info
+        self.container_description = container_description
+
+    @property
+    def resolve_dependencies(self):
+        return DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES if not self.container_description else self.container_description.resolve_dependencies
+
+    @property
+    def shell(self):
+        return DEFAULT_CONTAINER_SHELL if not self.container_description else self.container_description.shell
 
     @abstractmethod
     def containerize_command(self, command):
diff --git a/lib/galaxy/tools/deps/requirements.py b/lib/galaxy/tools/deps/requirements.py
index 452d9557e29c..2b209f63362d 100644
--- a/lib/galaxy/tools/deps/requirements.py
+++ b/lib/galaxy/tools/deps/requirements.py
@@ -1,4 +1,4 @@
-from galaxy.util import xml_text
+from galaxy.util import asbool, xml_text
 
 DEFAULT_REQUIREMENT_TYPE = "package"
 DEFAULT_REQUIREMENT_VERSION = None
@@ -27,22 +27,44 @@ def from_dict( dict ):
 
 
 DEFAULT_CONTAINER_TYPE = "docker"
+DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES = False
+DEFAULT_CONTAINER_SHELL = "/bin/sh"  # Galaxy assumes bash, but containers are usually thinner.
 
 
 class ContainerDescription( object ):
 
-    def __init__( self, identifier=None, type="docker" ):
+    def __init__(
+        self,
+        identifier=None,
+        type=DEFAULT_CONTAINER_TYPE,
+        resolve_dependencies=DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES,
+        shell=DEFAULT_CONTAINER_SHELL,
+    ):
         self.identifier = identifier
         self.type = type
+        self.resolve_dependencies = resolve_dependencies
+        self.shell = shell
 
     def to_dict( self ):
-        return dict(identifier=self.identifier, type=self.type)
+        return dict(
+            identifier=self.identifier,
+            type=self.type,
+            resolve_dependencies=self.resolve_dependencies,
+            shell=self.shell,
+        )
 
     @staticmethod
     def from_dict( dict ):
         identifier = dict["identifier"]
         type = dict.get("type", DEFAULT_CONTAINER_TYPE)
-        return ContainerDescription( identifier=identifier, type=type )
+        resolve_dependencies = dict.get("resolve_dependencies", DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES)
+        shell = dict.get("shell", DEFAULT_CONTAINER_SHELL)
+        return ContainerDescription(
+            identifier=identifier,
+            type=type,
+            resolve_dependencies=resolve_dependencies,
+            shell=shell,
+        )
 
 
 def parse_requirements_from_dict( root_dict ):
@@ -92,11 +114,20 @@ def parse_requirements_from_xml( xml_root ):
     if requirements_elem is not None:
         container_elems = requirements_elem.findall( 'container' )
 
-    containers = []
-    for container_elem in container_elems:
-        identifier = xml_text( container_elem )
-        type = container_elem.get( "type", DEFAULT_CONTAINER_TYPE )
-        container = ContainerDescription( identifier=identifier, type=type )
-        containers.append( container )
+    containers = map(container_from_element, container_elems)
 
     return requirements, containers
+
+
+def container_from_element(container_elem):
+    identifier = xml_text(container_elem)
+    type = container_elem.get("type", DEFAULT_CONTAINER_TYPE)
+    resolve_dependencies = asbool(container_elem.get("resolve_dependencies", DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES))
+    shell = container_elem.get("shell", DEFAULT_CONTAINER_SHELL)
+    container = ContainerDescription(
+        identifier=identifier,
+        type=type,
+        resolve_dependencies=resolve_dependencies,
+        shell=shell,
+    )
+    return container