Implement docker_galaxy engine type.

Specifying ``--engine docker_galaxy`` causes serve, test, and run operations to be backed with a Dockerized Galaxy instance powered by @bgruening's docker-galaxy-stable (https://github.com/bgruening/docker-galaxy-stable).

Requires various docker_util and command quoting improvements in galaxy-lib in 16.7.7 (galaxyproject/galaxy-lib@38eca73).

Fixes #15.

Author: jmchilton

planemo/docker.py

@@ -0,0 +1,13 @@
+"""Docker utilities for planemo.
+
+Built on Galaxy abstractions in :module:`galaxy.tools.deps.dockerfiles` and
+:module:`galaxy.tools.deps.docker_util`.
+"""
+from __future__ import absolute_import
+
+from galaxy.tools.deps.dockerfiles import docker_host_args
+
+
+__all__ = [
+    'docker_host_args',
+]

planemo/engine/factory.py

@@ -3,6 +3,7 @@
 import contextlib
 
 from .galaxy import GalaxyEngine
+from .galaxy import DockerizedGalaxyEngine
 from .cwltool import CwlToolEngine
 
 UNKNOWN_ENGINE_TYPE_MESSAGE = "Unknown engine type specified [%s]."
@@ -17,9 +18,10 @@ def is_galaxy_engine(**kwds):
 def build_engine(ctx, **kwds):
     """Build an engine from the supplied planemo configuration."""
     engine_type_str = kwds.get("engine", "galaxy")
-
     if engine_type_str == "galaxy":
         engine_type = GalaxyEngine
+    elif engine_type == "dockerize_galaxy":
+        engine_type = DockerizedGalaxyEngine
     elif engine_type_str == "cwltool":
         engine_type = CwlToolEngine
     else:

planemo/engine/galaxy.py

@@ -31,8 +31,23 @@ def _run(self, runnable, job_path):
 
     @contextlib.contextmanager
     def _serve(self, runnables):
-        with serve_daemon(self._ctx, runnables, **self._kwds) as config:
+        with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
             yield config
 
+    def _serve_kwds(self):
+        return self._kwds.copy()
 
-__all__ = ["GalaxyEngine"]
+
+class DockerizedGalaxyEngine(GalaxyEngine):
+    """An :class:`Engine` implementation backed by Galaxy running in Docker.
+
+    More information on Galaxy can be found at http://galaxyproject.org/.
+    """
+
+    def _serve_kwds(self):
+        serve_kwds = self._kwds.copy()
+        serve_kwds["dockerize"] = True
+        return serve_kwds
+
+
+__all__ = ["GalaxyEngine", "DockerizedGalaxyEngine"]