HTCondor Docker Integration

config/job_conf.xml.sample_advanced

@@ -434,6 +434,26 @@
                  <param> tags.
             -->
             <param id="request_cpus">8</param>
+
+            <!-- Recent version of HTCondor do have a `docker` universe to handle containers.
+                 Activate this feature by explicitly specifying the `docker` universe.
+            -->
+            <!-- <param id="universe">docker</param> -->
+
+            <!-- If the tool has a container specified this one is used.
+
+                <requirements>
+                    <container type="docker">bgruening/galaxy-stable</container>
+                </requirements>
+
+            Unless the job destination specifies an override 
+            with docker_container_id_override. If neither of 
+            these is set a default container can be specified
+            with docker_default_container_id. The resolved
+            container ID will be passed along to condor as
+            the docker_image submission parameter.
+            -->
+            <!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
         </destination>
 
         <!-- Jobs that hit the walltime on one destination can be automatically

lib/galaxy/jobs/__init__.py

@@ -413,7 +413,15 @@ def __get_default(self, parent, names):
 
         :returns: str -- id or tag representing the default.
         """
+
         rval = parent.get('default')
+        if 'default_from_environ' in parent.attrib:
+            environ_var = parent.attrib['default_from_environ']
+            rval = os.environ.get(environ_var, rval)
+        elif 'default_from_config' in parent.attrib:
+            config_val = parent.attrib['default_from_config']
+            rval = self.app.config.config_dict.get(config_val, rval)
+
         if rval is not None:
             # If the parent element has a 'default' attribute, use the id or tag in that attribute
             if rval not in names:

lib/galaxy/jobs/runners/condor.py

@@ -57,6 +57,14 @@ def queue_job( self, job_wrapper ):
 
         # get destination params
         query_params = submission_params(prefix="", **job_destination.params)
+        container = None
+        universe = query_params.get('universe', False)
+        if universe.strip().lower() == 'docker':
+            container = self.find_container( job_wrapper )
+            if container:
+                # HTCondor needs the image as 'docker_image'
+                query_params.update({'docker_image': container})
+
         galaxy_slots = query_params.get('request_cpus', None)
         if galaxy_slots:
             galaxy_slots_statement = 'GALAXY_SLOTS="%s"; export GALAXY_SLOTS_CONFIGURED="1"' % galaxy_slots

lib/galaxy/tools/deps/containers.py

@@ -107,7 +107,11 @@ def __overridden_container_id(self, container_type, destination_info):
     def __default_container_id(self, container_type, destination_info):
         if not self.__container_type_enabled(container_type, destination_info):
             return None
-        return destination_info.get("%s_default_container_id" % container_type)
+        key = "%s_default_container_id" % container_type
+        # Also allow docker_image...
+        if key not in destination_info:
+            key = "%s_image" % container_type
+        return destination_info.get(key)
 
     def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info):
         # TODO: ensure destination_info is dict-like